rs10136427

Variant names:

• chr14-75513546-C-T
• rs10136427
• ENST00000751543.1:n.74-15132G>A

Variant summary

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

The ENST00000751543.1(ENSG00000297883):​n.74-15132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,112 control chromosomes in the GnomAD database, including 3,486 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 0.21 (3486 hom., cov: 31)
• Consequence: ENSG00000297883 ENST00000751543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 11 publications found

Genes affected

ENSG00000297883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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
ENSG00000297883	ENST00000751543.1	n.74-15132G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31216 AN: 151992 Hom.: 3474 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.205 AC: 31247 AN: 152112 Hom.: 3486 Cov.: 31 AF XY: 0.215 AC XY: 15959 AN XY: 74362

African (AFR) AF: 0.154 AC: 6410 AN: 41520

American (AMR) AF: 0.265 AC: 4055 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5174

South Asian (SAS) AF: 0.154 AC: 744 AN: 4830

European-Finnish (FIN) AF: 0.374 AC: 3943 AN: 10550

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13961 AN: 67970

Other (OTH) AF: 0.180 AC: 380 AN: 2112

Alfa AF: 0.195 Hom.: 3584

Bravo AF: 0.196

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.88
DANN	Benign	0.59
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10136427; hg19: chr14-75979889;