rs1984620

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000577743.2(MYHAS):​n.95+5118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,006 control chromosomes in the GnomAD database, including 10,433 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10433 hom., cov: 32)

Consequence

MYHAS
ENST00000577743.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.474

Publications

3 publications found
Variant links:
Genes affected
MYHAS (HGNC:50609): (myosin heavy chain gene cluster antisense RNA) Predicted to enable primary miRNA binding activity. Predicted to be involved in response to muscle activity and skeletal muscle fiber development. Predicted to act upstream of or within with a positive effect on gene expression. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC107985004XR_001752791.3 linkn.95+5118G>A intron_variant Intron 1 of 4
LOC107985004XR_007065617.1 linkn.95+5118G>A intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYHASENST00000577743.2 linkn.95+5118G>A intron_variant Intron 1 of 3 2
MYHASENST00000609088.1 linkn.94+5118G>A intron_variant Intron 1 of 1 4
MYHASENST00000715354.1 linkn.97+5118G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.356
AC:
54102
AN:
151888
Hom.:
10436
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.228
Gnomad AMI
AF:
0.524
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.370
Gnomad EAS
AF:
0.220
Gnomad SAS
AF:
0.240
Gnomad FIN
AF:
0.442
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.447
Gnomad OTH
AF:
0.348
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.356
AC:
54121
AN:
152006
Hom.:
10433
Cov.:
32
AF XY:
0.351
AC XY:
26050
AN XY:
74306
show subpopulations
African (AFR)
AF:
0.228
AC:
9432
AN:
41440
American (AMR)
AF:
0.310
AC:
4740
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.370
AC:
1283
AN:
3470
East Asian (EAS)
AF:
0.220
AC:
1138
AN:
5172
South Asian (SAS)
AF:
0.241
AC:
1162
AN:
4822
European-Finnish (FIN)
AF:
0.442
AC:
4675
AN:
10568
Middle Eastern (MID)
AF:
0.337
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
0.447
AC:
30380
AN:
67950
Other (OTH)
AF:
0.348
AC:
734
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1713
3426
5139
6852
8565
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
532
1064
1596
2128
2660
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.411
Hom.:
22325
Bravo
AF:
0.341
Asia WGS
AF:
0.239
AC:
833
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.6
DANN
Benign
0.83
PhyloP100
-0.47

Splicing

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

Publications

Other links and lift over

dbSNP: rs1984620; hg19: chr17-10200348; API