rs10510706

Variant names:

• chr3-40058766-T-A
• rs10510706
• NM_015460.4:c.332+14495T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-40058766-T-A
• chr3-40058766-T-C

Variant summary

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

The NM_015460.4(MYRIP):​c.332+14495T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,980 control chromosomes in the GnomAD database, including 6,494 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 0.29 (6494 hom., cov: 32)
• Consequence: MYRIP NM_015460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 4 publications found

Genes affected

MYRIP (HGNC:19156): (myosin VIIA and Rab interacting protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be involved in positive regulation of insulin secretion. Predicted to be located in actin cytoskeleton; dense core granule; and perinuclear region of cytoplasm. Predicted to be part of exocyst. Predicted to be active in cortical actin cytoskeleton. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYRIP	NM_015460.4	c.332+14495T>A		intron_variant	Intron 3 of 16	ENST00000302541.11	NP_056275.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYRIP	ENST00000302541.11	c.332+14495T>A		intron_variant	Intron 3 of 16	1	NM_015460.4	ENSP00000301972.6

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44114 AN: 151864 Hom.: 6495 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.290 AC: 44132 AN: 151980 Hom.: 6494 Cov.: 32 AF XY: 0.291 AC XY: 21620 AN XY: 74302

African (AFR) AF: 0.296 AC: 12251 AN: 41428

American (AMR) AF: 0.290 AC: 4427 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1835 AN: 5164

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2801 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18881 AN: 67970

Other (OTH) AF: 0.297 AC: 627 AN: 2114

Alfa AF: 0.286 Hom.: 774

Bravo AF: 0.294

Asia WGS AF: 0.356 AC: 1236 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	1.4
DANN	Benign	0.30
PhyloP100		-0.59
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: rs10510706; hg19: chr3-40100257;