17-32610729-A-T

Position:

• chr17-32610729-A-T

Variant summary

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

The NM_015194.3(MYO1D):​c.2710-5488T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,972 control chromosomes in the GnomAD database, including 20,447 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 0.51 (20447 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2710-5488T>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.2710-5488T>A		intron_variant		1	NM_015194.3	ENSP00000324527	P1
MYO1D	ENST00000394649.8	c.2446-5488T>A		intron_variant		5		ENSP00000464741
MYO1D	ENST00000579584.5	c.2710-5488T>A		intron_variant		2		ENSP00000464305
MYO1D	ENST00000577352.5	n.657-5488T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77615 AN: 151854 Hom.: 20410 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.511 AC: 77698 AN: 151972 Hom.: 20447 Cov.: 32 AF XY: 0.503 AC XY: 37352 AN XY: 74284

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.517

Alfa AF: 0.361 Hom.: 843

Bravo AF: 0.522

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.020
DANN	Benign	0.72

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: rs2055091; hg19: chr17-30937747;