rs1143625

Variant names:

• chr2-112837782-T-C
• rs1143625
• ENST00000762706.1:n.405-47476T>C

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-47476T>C 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 150,700 control chromosomes in the GnomAD database, including 5,500 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 0.25 (5500 hom., cov: 28)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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.405-47476T>C		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-47476T>C		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-47476T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37552 AN: 150598 Hom.: 5480 Cov.: 28

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.166

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: 37594 AN: 150700 Hom.: 5500 Cov.: 28 AF XY: 0.258 AC XY: 19007 AN XY: 73564

African (AFR) AF: 0.108 AC: 4439 AN: 41016

American (AMR) AF: 0.401 AC: 6076 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3462

East Asian (EAS) AF: 0.415 AC: 2098 AN: 5058

South Asian (SAS) AF: 0.358 AC: 1701 AN: 4756

European-Finnish (FIN) AF: 0.334 AC: 3446 AN: 10324

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18256 AN: 67630

Other (OTH) AF: 0.254 AC: 534 AN: 2100

Alfa AF: 0.253 Hom.: 677

Bravo AF: 0.248

Asia WGS AF: 0.383 AC: 1333 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.52
PhyloP100		0.20

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: rs1143625;

hg19: chr2-113595359;