rs13031703

Variant names:

• chr2-127129099-C-T
• rs13031703
• ENST00000726607.1:n.342-6161C>T

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-6161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,210 control chromosomes in the GnomAD database, including 1,168 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 0.12 (1168 hom., cov: 33)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 10 publications found

Genes affected

ENSG00000294899 (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 (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. 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
	ENSG00000294899	ENST00000726607.1		n.342-6161C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17759 AN: 152092 Hom.: 1169 Cov.: 33

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.117 AC: 17761 AN: 152210 Hom.: 1168 Cov.: 33 AF XY: 0.120 AC XY: 8896 AN XY: 74412

African (AFR) AF: 0.0683 AC: 2839 AN: 41548

American (AMR) AF: 0.105 AC: 1603 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 296 AN: 3468

East Asian (EAS) AF: 0.113 AC: 588 AN: 5188

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4818

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9168 AN: 68006

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.130 Hom.: 1808

Bravo AF: 0.105

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.29

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: rs13031703;

hg19: chr2-127886675;