17-32565336-C-T

Variant names:

• chr17-32565336-C-T
• rs372501
• NM_015194.3:c.2864+39751G>A

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+39751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,086 control chromosomes in the GnomAD database, including 17,684 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 0.47 (17684 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2864+39751G>A		intron_variant	Intron 21 of 21	ENST00000318217.10	NP_056009.1
MYO1D	NM_001411088.1	c.2600+39751G>A		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+39751G>A		intron_variant	Intron 21 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000394649.8	c.2600+39751G>A		intron_variant	Intron 23 of 23	5		ENSP00000464741.1
MYO1D	ENST00000577352.5	n.811+39751G>A		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72179 AN: 151966 Hom.: 17667 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.475 AC: 72239 AN: 152086 Hom.: 17684 Cov.: 32 AF XY: 0.478 AC XY: 35513 AN XY: 74366

African (AFR) AF: 0.590 AC: 24462 AN: 41452

American (AMR) AF: 0.465 AC: 7108 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.546 AC: 2814 AN: 5154

South Asian (SAS) AF: 0.486 AC: 2344 AN: 4828

European-Finnish (FIN) AF: 0.431 AC: 4564 AN: 10594

Middle Eastern (MID) AF: 0.434 AC: 126 AN: 290

European-Non Finnish (NFE) AF: 0.407 AC: 27700 AN: 67982

Other (OTH) AF: 0.484 AC: 1024 AN: 2114

Alfa AF: 0.398 Hom.: 3629

Bravo AF: 0.481

Asia WGS AF: 0.557 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		0.10
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: rs372501; hg19: chr17-30892354;