rs2313132

Variant names:

• chr4-137771096-G-A
• rs2313132
• ENST00000765862.1:n.330-36098C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-137771096-G-A
• chr4-137771096-G-T

Variant summary

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

The ENST00000765862.1(ENSG00000250126):​n.330-36098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,160 control chromosomes in the GnomAD database, including 63,191 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 0.91 (63191 hom., cov: 29)
• Consequence: ENSG00000250126 ENST00000765862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 14 publications found

Genes affected

ENSG00000250126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765862.1. 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
	ENSG00000250126	ENST00000765862.1		n.330-36098C>T		intron	N/A
	ENSG00000250126	ENST00000765863.1		n.330-36098C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138436 AN: 152042 Hom.: 63140 Cov.: 29

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.911 AC: 138546 AN: 152160 Hom.: 63191 Cov.: 29 AF XY: 0.910 AC XY: 67689 AN XY: 74384

African (AFR) AF: 0.946 AC: 39291 AN: 41542

American (AMR) AF: 0.941 AC: 14380 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3205 AN: 3470

East Asian (EAS) AF: 0.967 AC: 4992 AN: 5164

South Asian (SAS) AF: 0.939 AC: 4520 AN: 4816

European-Finnish (FIN) AF: 0.851 AC: 9000 AN: 10582

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60056 AN: 67990

Other (OTH) AF: 0.916 AC: 1933 AN: 2110

Alfa AF: 0.899 Hom.: 164094

Bravo AF: 0.918

Asia WGS AF: 0.935 AC: 3251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.73
PhyloP100		-0.72

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: rs2313132;

hg19: chr4-138692250;