rs1911014

Variant names:

• chr4-125852943-G-A
• rs1911014
• ENST00000667497.1:n.163+100277G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-125852943-G-A
• chr4-125852943-G-C

Variant summary

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

The ENST00000667497.1(ENSG00000250149):​n.163+100277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,044 control chromosomes in the GnomAD database, including 1,507 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 0.13 (1507 hom., cov: 32)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 5 publications found

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667497.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250149	ENST00000667497.1		n.163+100277G>A		intron	N/A
	ENSG00000300351	ENST00000771109.1		n.212+6853G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19964 AN: 151926 Hom.: 1505 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.131 AC: 19968 AN: 152044 Hom.: 1507 Cov.: 32 AF XY: 0.133 AC XY: 9874 AN XY: 74320

African (AFR) AF: 0.0745 AC: 3091 AN: 41500

American (AMR) AF: 0.0978 AC: 1494 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.101 AC: 522 AN: 5174

South Asian (SAS) AF: 0.104 AC: 501 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10546

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11016 AN: 67940

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.146 Hom.: 1790

Bravo AF: 0.121

Asia WGS AF: 0.101 AC: 351 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.59
PhyloP100		0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1911014;

hg19: chr4-126774098;

COSMIC: COSV68632466;