rs16936517

Variant names:

• chr10-37444453-C-T
• rs16936517
• ENST00000755343.1:n.258-1241C>T

Variant summary

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

The ENST00000755343.1(ENSG00000298408):​n.258-1241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,136 control chromosomes in the GnomAD database, including 982 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 0.10 (982 hom., cov: 32)
• Consequence: ENSG00000298408 ENST00000755343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 0 publications found

Genes affected

ENSG00000298408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298408	ENST00000755343.1	n.258-1241C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15540 AN: 152018 Hom.: 954 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0749

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.103 AC: 15620 AN: 152136 Hom.: 982 Cov.: 32 AF XY: 0.102 AC XY: 7602 AN XY: 74368

African (AFR) AF: 0.165 AC: 6844 AN: 41468

American (AMR) AF: 0.0654 AC: 1001 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.154 AC: 795 AN: 5164

South Asian (SAS) AF: 0.0743 AC: 358 AN: 4818

European-Finnish (FIN) AF: 0.0655 AC: 694 AN: 10594

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5317 AN: 68010

Other (OTH) AF: 0.105 AC: 221 AN: 2108

Alfa AF: 0.0833 Hom.: 866

Bravo AF: 0.107

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.091
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs16936517; hg19: chr10-37733381;