chr17-32569437-C-T

Variant names:

• chr17-32569437-C-T
• rs225212
• NM_015194.3:c.2864+35650G>A

Variant summary

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

The NM_015194.3(MYO1D):​c.2864+35650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,036 control chromosomes in the GnomAD database, including 14,692 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 0.44 (14692 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2864+35650G>A		intron_variant	Intron 21 of 21	ENST00000318217.10	NP_056009.1
MYO1D	NM_001411088.1	c.2600+35650G>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+35650G>A		intron_variant	Intron 21 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000394649.8	c.2600+35650G>A		intron_variant	Intron 23 of 23	5		ENSP00000464741.1
MYO1D	ENST00000577352.5	n.811+35650G>A		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66252 AN: 151918 Hom.: 14674 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.436 AC: 66314 AN: 152036 Hom.: 14692 Cov.: 32 AF XY: 0.439 AC XY: 32642 AN XY: 74316

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.446

Alfa AF: 0.416 Hom.: 2253

Bravo AF: 0.442

Asia WGS AF: 0.527 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.0090
DANN	Benign	0.33

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: rs225212; hg19: chr17-30896455;