2-112838252-C-G

Variant names:

• chr2-112838252-C-G
• rs1143623
• ENST00000762706.1:n.405-47006C>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-47006C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,044 control chromosomes in the GnomAD database, including 5,511 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.25 (5511 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.0710
• Publications: 194 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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.405-47006C>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-47006C>G		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-47006C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37764 AN: 151926 Hom.: 5490 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.249 AC: 37808 AN: 152044 Hom.: 5511 Cov.: 31 AF XY: 0.258 AC XY: 19147 AN XY: 74306

African (AFR) AF: 0.108 AC: 4481 AN: 41484

American (AMR) AF: 0.399 AC: 6102 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2073 AN: 5162

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3520 AN: 10544

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18337 AN: 67976

Other (OTH) AF: 0.254 AC: 536 AN: 2108

Alfa AF: 0.254 Hom.: 676

Bravo AF: 0.247

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Antisynthetase syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.29
PhyloP100		0.071

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: rs1143623;

hg19: chr2-113595829;

COSMIC: COSV54521326;