6-75749422-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_004999.4(MYO6):​c.-49C>G variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 152,992 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.018 ( 44 hom., cov: 31)
Exomes 𝑓: 0.013 ( 2 hom. )

Consequence

MYO6
NM_004999.4 splice_region, 5_prime_UTR

Scores

2
Splicing: ADA: 0.0003703
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: -0.593
Variant links:
Genes affected
MYO6 (HGNC:7605): (myosin VI) This gene encodes a reverse-direction motor protein that moves toward the minus end of actin filaments and plays a role in intracellular vesicle and organelle transport. The protein consists of a motor domain containing an ATP- and an actin-binding site and a globular tail which interacts with other proteins. This protein maintains the structural integrity of inner ear hair cells and mutations in this gene cause non-syndromic autosomal dominant and recessive hearing loss. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 6-75749422-C-G is Benign according to our data. Variant chr6-75749422-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 357987.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=1}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0182 (2771/152316) while in subpopulation NFE AF= 0.0287 (1950/68022). AF 95% confidence interval is 0.0276. There are 44 homozygotes in gnomad4. There are 1273 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 44 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYO6NM_004999.4 linkuse as main transcriptc.-49C>G splice_region_variant, 5_prime_UTR_variant 1/35 ENST00000369977.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYO6ENST00000369977.8 linkuse as main transcriptc.-49C>G splice_region_variant, 5_prime_UTR_variant 1/351 NM_004999.4 A1Q9UM54-1

Frequencies

GnomAD3 genomes
AF:
0.0182
AC:
2770
AN:
152198
Hom.:
44
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00564
Gnomad AMI
AF:
0.0319
Gnomad AMR
AF:
0.0179
Gnomad ASJ
AF:
0.0392
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00621
Gnomad FIN
AF:
0.00546
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0286
Gnomad OTH
AF:
0.0186
GnomAD4 exome
AF:
0.0133
AC:
9
AN:
676
Hom.:
2
Cov.:
0
AF XY:
0.0110
AC XY:
6
AN XY:
546
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0156
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0182
AC:
2771
AN:
152316
Hom.:
44
Cov.:
31
AF XY:
0.0171
AC XY:
1273
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.00563
Gnomad4 AMR
AF:
0.0179
Gnomad4 ASJ
AF:
0.0392
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00622
Gnomad4 FIN
AF:
0.00546
Gnomad4 NFE
AF:
0.0287
Gnomad4 OTH
AF:
0.0189
Alfa
AF:
0.0203
Hom.:
11
Bravo
AF:
0.0187
Asia WGS
AF:
0.00318
AC:
11
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 37 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMay 15, 2021- -
Autosomal dominant nonsyndromic hearing loss 22 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
CADD
Benign
7.3
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00037
dbscSNV1_RF
Benign
0.014
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149130280; hg19: chr6-76459139; API