rs379123

chr17-32564796-T-C

Variant summary

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

The NM_015194.3(MYO1D):c.2864+40291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,928 control chromosomes in the GnomAD database, including 19,374 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 0.49 (19374 hom., cov: 31)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1D	NM_015194.3	c.2864+40291A>G		intron_variant		ENST00000318217.10
MYO1D	NM_001411088.1	c.2600+40291A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1D	ENST00000318217.10	c.2864+40291A>G		intron_variant		1	NM_015194.3	P1
MYO1D	ENST00000394649.8	c.2600+40291A>G		intron_variant		5
MYO1D	ENST00000577352.5	n.811+40291A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75014 AN: 151810 Hom.: 19352 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.494 AC: 75079 AN: 151928 Hom.: 19374 Cov.: 31 AF XY: 0.496 AC XY: 36809 AN XY: 74264

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.504

Alfa AF: 0.434 Hom.: 10770

Bravo AF: 0.503

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.042
Dann	Benign	0.47

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: rs379123; hg19: chr17-30891814; COSMIC: COSV59019536;