2-112798015-C-T

Variant names:

• chr2-112798015-C-T
• rs11687624
• ENST00000762706.1:n.404+27119C>T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+27119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,672 control chromosomes in the GnomAD database, including 22,082 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 0.54 (22082 hom., cov: 30)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 7 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
	ENSG00000299339	ENST00000762706.1		n.404+27119C>T		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+27119C>T		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+27119C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81138 AN: 151554 Hom.: 22067 Cov.: 30

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.535 AC: 81190 AN: 151672 Hom.: 22082 Cov.: 30 AF XY: 0.531 AC XY: 39353 AN XY: 74090

African (AFR) AF: 0.508 AC: 20987 AN: 41302

American (AMR) AF: 0.497 AC: 7572 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1491 AN: 5154

South Asian (SAS) AF: 0.526 AC: 2527 AN: 4806

European-Finnish (FIN) AF: 0.512 AC: 5376 AN: 10492

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39124 AN: 67908

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.558 Hom.: 72144

Bravo AF: 0.527

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.28

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: rs11687624;

hg19: chr2-113555592;