chr17-32792019-A-G

Variant names:

• chr17-32792019-A-G
• rs17780981
• NM_015194.3:c.96-11235T>C

Variant summary

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

The NM_015194.3(MYO1D):​c.96-11235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,210 control chromosomes in the GnomAD database, including 2,044 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 (2044 hom., cov: 32)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 11 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=-0.83).
• 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 rank	MANE	Protein	UniProt
MYO1D	NM_015194.3	c.96-11235T>C		intron_variant	Intron 1 of 21	ENST00000318217.10	NP_056009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1D	ENST00000318217.10	c.96-11235T>C		intron_variant	Intron 1 of 21	1	NM_015194.3	ENSP00000324527.5
MYO1D	ENST00000583621.1	c.96-11235T>C		intron_variant	Intron 1 of 10	1		ENSP00000462055.1
MYO1D	ENST00000579584.5	c.96-11235T>C		intron_variant	Intron 1 of 21	2		ENSP00000464305.1
MYO1D	ENST00000394649.8	c.-170+445T>C		intron_variant	Intron 3 of 23	5		ENSP00000464741.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22022 AN: 152092 Hom.: 2041 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00653

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.145 AC: 22028 AN: 152210 Hom.: 2044 Cov.: 32 AF XY: 0.142 AC XY: 10600 AN XY: 74390

African (AFR) AF: 0.0404 AC: 1677 AN: 41560

American (AMR) AF: 0.176 AC: 2696 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3470

East Asian (EAS) AF: 0.00655 AC: 34 AN: 5192

South Asian (SAS) AF: 0.206 AC: 991 AN: 4818

European-Finnish (FIN) AF: 0.171 AC: 1805 AN: 10578

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13344 AN: 67988

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.173 Hom.: 319

Bravo AF: 0.139

Asia WGS AF: 0.105 AC: 366 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		1.2
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: rs17780981; hg19: chr17-31119037;