Variant rs3751624 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018728.4(MYO5C):c.28-81G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 902,972 control chromosomes in the GnomAD database, including 14,742 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 0.20 ( 3287 hom., cov: 32)

Exomes 𝑓: 0.17 ( 11455 hom. )

Consequence

MYO5C
NM_018728.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.776

Variant links:

Genes affected

MYO5C (HGNC:7604): (myosin VC) Predicted to enable actin filament binding activity and microfilament motor activity. Predicted to be involved in actin filament organization and vesicle transport along actin filament. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

MYO5C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
MYO5C	NM_018728.4 linkuse as main transcript	c.28-81G>A	intron_variant	ENST00000261839.12	NP_061198.2
MYO5C	XM_011521781.4 linkuse as main transcript	c.28-81G>A	intron_variant		XP_011520083.1
MYO5C	XM_017022408.3 linkuse as main transcript	c.28-81G>A	intron_variant		XP_016877897.1
MYO5C	XM_047432845.1 linkuse as main transcript	c.28-81G>A	intron_variant		XP_047288801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO5C	ENST00000261839.12 linkuse as main transcript	c.28-81G>A		intron_variant		1	NM_018728.4	ENSP00000261839	P1	Q9NQX4-1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29803

AN:

152052

Hom.:

3282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.274

Gnomad EAS

AF:

0.0906

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.0959

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.194

GnomAD4 exome

AF:

0.168

AC:

125799

AN:

750802

Hom.:

11455

AF XY:

0.170

AC XY:

67140

AN XY:

395722

show subpopulations

Gnomad4 AFR exome

AF:

0.291

Gnomad4 AMR exome

AF:

0.131

Gnomad4 ASJ exome

AF:

0.268

Gnomad4 EAS exome

AF:

0.0633

Gnomad4 SAS exome

AF:

0.205

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.196

AC:

29831

AN:

152170

Hom.:

3287

Cov.:

AF XY:

0.191

AC XY:

14240

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.158

Gnomad4 ASJ

AF:

0.274

Gnomad4 EAS

AF:

0.0908

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.0959

Gnomad4 NFE

AF:

0.163

Gnomad4 OTH

AF:

0.196

Alfa

AF:

0.173

Hom.:

4802

Bravo

AF:

0.203

Asia WGS

AF:

0.160

AC:

557

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over