chr17-32751254-C-T

Position:

• chr17-32751254-C-T

Variant summary

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

The NM_015194.3(MYO1D):​c.1468-2248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,140 control chromosomes in the GnomAD database, including 2,025 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 0.14 (2025 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.1468-2248G>A		intron_variant		ENST00000318217.10	NP_056009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO1D	ENST00000318217.10	c.1468-2248G>A		intron_variant		1	NM_015194.3	ENSP00000324527	P1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21906 AN: 152022 Hom.: 2022 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00576

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.144 AC: 21914 AN: 152140 Hom.: 2025 Cov.: 32 AF XY: 0.142 AC XY: 10548 AN XY: 74364

Gnomad4 AFR AF: 0.0401

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.00578

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.172

Alfa AF: 0.170 Hom.: 423

Bravo AF: 0.138

Asia WGS AF: 0.106 AC: 367 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.69

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: rs17183295; hg19: chr17-31078272;