NM_015194.3:c.2121+9881C>T

Variant names:

• chr17-32702107-G-A
• rs17183113
• NM_015194.3:c.2121+9881C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015194.3(MYO1D):​c.2121+9881C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,166 control chromosomes in the GnomAD database, including 1,987 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 (1987 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.2121+9881C>T		intron_variant	Intron 16 of 21	ENST00000318217.10	NP_056009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1D	ENST00000318217.10	c.2121+9881C>T		intron_variant	Intron 16 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000579584.5	c.2121+9881C>T		intron_variant	Intron 16 of 21	2		ENSP00000464305.1
MYO1D	ENST00000394649.8	c.1857+9881C>T		intron_variant	Intron 18 of 23	5		ENSP00000464741.1
MYO1D	ENST00000585094.1	n.321+9881C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21693 AN: 152048 Hom.: 1984 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.143 AC: 21702 AN: 152166 Hom.: 1987 Cov.: 32 AF XY: 0.141 AC XY: 10459 AN XY: 74378

African (AFR) AF: 0.0401 AC: 1666 AN: 41530

American (AMR) AF: 0.175 AC: 2680 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5188

South Asian (SAS) AF: 0.204 AC: 986 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1788 AN: 10558

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13098 AN: 67984

Other (OTH) AF: 0.172 AC: 363 AN: 2116

Alfa AF: 0.169 Hom.: 298

Bravo AF: 0.137

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.57
PhyloP100		0.54
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: rs17183113; hg19: chr17-31029125;