2-162974850-C-T

Variant names:

• chr2-162974850-C-T
• rs11900934
• ENST00000724875.1:n.266-3365G>A

Variant summary

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

The ENST00000724875.1(ENSG00000294636):​n.266-3365G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,348 control chromosomes in the GnomAD database, including 6,785 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 0.28 (6785 hom., cov: 32)
• Consequence: ENSG00000294636 ENST00000724875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 5 publications found

Genes affected

ENSG00000294636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724875.1. 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
	ENSG00000294636	ENST00000724875.1		n.266-3365G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43038 AN: 151228 Hom.: 6775 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.285 AC: 43074 AN: 151348 Hom.: 6785 Cov.: 32 AF XY: 0.276 AC XY: 20427 AN XY: 73926

African (AFR) AF: 0.406 AC: 16801 AN: 41336

American (AMR) AF: 0.196 AC: 2976 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 847 AN: 3454

East Asian (EAS) AF: 0.188 AC: 963 AN: 5124

South Asian (SAS) AF: 0.162 AC: 778 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10602

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17770 AN: 67560

Other (OTH) AF: 0.278 AC: 583 AN: 2100

Alfa AF: 0.254 Hom.: 5970

Bravo AF: 0.293

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11900934; hg19: chr2-163831360;