chr17-32564796-T-C

Variant names:

• chr17-32564796-T-C
• rs379123
• NM_015194.3:c.2864+40291A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015194.3(MYO1D):​c.2864+40291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,928 control chromosomes in the GnomAD database, including 19,374 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 0.49 (19374 hom., cov: 31)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 11 publications found

Genes affected

MYO1D (HGNC:7598): (myosin ID) Enables protein domain specific binding activity. Predicted to be involved in actin filament organization; early endosome to recycling endosome transport; and vesicle transport along actin filament. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2864+40291A>G		intron_variant	Intron 21 of 21	ENST00000318217.10	NP_056009.1
MYO1D	NM_001411088.1	c.2600+40291A>G		intron_variant	Intron 22 of 22		NP_001398017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1D	ENST00000318217.10	c.2864+40291A>G		intron_variant	Intron 21 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000394649.8	c.2600+40291A>G		intron_variant	Intron 23 of 23	5		ENSP00000464741.1
MYO1D	ENST00000577352.5	n.811+40291A>G		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75014 AN: 151810 Hom.: 19352 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.502

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.494 AC: 75079 AN: 151928 Hom.: 19374 Cov.: 31 AF XY: 0.496 AC XY: 36809 AN XY: 74264

African (AFR) AF: 0.653 AC: 27041 AN: 41436

American (AMR) AF: 0.479 AC: 7299 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2804 AN: 5148

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4548 AN: 10564

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27739 AN: 67928

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.437 Hom.: 32625

Bravo AF: 0.503

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.042
DANN	Benign	0.47
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs379123; hg19: chr17-30891814; COSMIC: COSV59019536;