17-32610729-A-T

Variant names:

• chr17-32610729-A-T
• rs2055091
• NM_015194.3:c.2710-5488T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015194.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1D	NM_015194.3	MANE Select	c.2710-5488T>A		intron	N/A	NP_056009.1
	MYO1D	NM_001303279.2		c.2710-5488T>A		intron	N/A	NP_001290208.1
	MYO1D	NM_001411088.1		c.2446-5488T>A		intron	N/A	NP_001398017.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1D	ENST00000318217.10	TSL:1 MANE Select	c.2710-5488T>A		intron	N/A	ENSP00000324527.5
	MYO1D	ENST00000579584.5	TSL:2	c.2710-5488T>A		intron	N/A	ENSP00000464305.1
	MYO1D	ENST00000394649.8	TSL:5	c.2446-5488T>A		intron	N/A	ENSP00000464741.1

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

African (AFR) AF: 0.577 AC: 23890 AN: 41430

American (AMR) AF: 0.482 AC: 7362 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1248 AN: 5162

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4818

European-Finnish (FIN) AF: 0.346 AC: 3655 AN: 10574

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35307 AN: 67936

Other (OTH) AF: 0.517 AC: 1090 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.020
DANN	Benign	0.72
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2055091; hg19: chr17-30937747;