13-108498881-C-T

Variant names:

• chr13-108498881-C-T
• rs2391644
• ENST00000757457.1:n.43+2957C>T

Variant summary

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

The ENST00000757457.1(ENSG00000298702):​n.43+2957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,910 control chromosomes in the GnomAD database, including 11,184 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 0.38 (11184 hom., cov: 32)
• Consequence: ENSG00000298702 ENST00000757457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 2 publications found

Genes affected

ENSG00000298702 (HGNC:):

MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	XM_011521062.2	c.-39+2957C>T		intron_variant	Intron 1 of 34		XP_011519364.1
MYO16	XM_047430183.1	c.-39+2957C>T		intron_variant	Intron 1 of 34		XP_047286139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298702	ENST00000757457.1	n.43+2957C>T		intron_variant	Intron 1 of 1
ENSG00000298702	ENST00000757458.1	n.91+2882C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57489 AN: 151792 Hom.: 11183 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.379 AC: 57514 AN: 151910 Hom.: 11184 Cov.: 32 AF XY: 0.387 AC XY: 28749 AN XY: 74220

African (AFR) AF: 0.382 AC: 15816 AN: 41404

American (AMR) AF: 0.427 AC: 6514 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2603 AN: 5138

South Asian (SAS) AF: 0.476 AC: 2295 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4688 AN: 10562

Middle Eastern (MID) AF: 0.472 AC: 137 AN: 290

European-Non Finnish (NFE) AF: 0.334 AC: 22681 AN: 67944

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.349 Hom.: 26805

Bravo AF: 0.375

Asia WGS AF: 0.518 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.44
DANN	Benign	0.18
PhyloP100		-0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2391644; hg19: chr13-109151229;