17-32508752-C-T

Variant names:

• chr17-32508752-C-T
• rs2519866
• NM_015194.3:c.2865-13837G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015194.3(MYO1D):​c.2865-13837G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,100 control chromosomes in the GnomAD database, including 33,174 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 0.66 (33174 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2865-13837G>A		intron_variant	Intron 21 of 21	ENST00000318217.10	NP_056009.1
MYO1D	NM_001411088.1	c.2601-13837G>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.2865-13837G>A		intron_variant	Intron 21 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000394649.8	c.2601-13837G>A		intron_variant	Intron 23 of 23	5		ENSP00000464741.1
MYO1D	ENST00000577352.5	n.812-13837G>A		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99995 AN: 151980 Hom.: 33152 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.658 AC: 100066 AN: 152100 Hom.: 33174 Cov.: 32 AF XY: 0.660 AC XY: 49049 AN XY: 74344

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.632

Alfa AF: 0.683 Hom.: 49028

Bravo AF: 0.655

Asia WGS AF: 0.644 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs2519866; hg19: chr17-30835770;