rs4667682

Variant names:

• chr2-171271410-C-T
• rs4667682
• ENST00000796848.1:n.150-68G>A

Variant summary

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

The ENST00000796848.1(ENSG00000303737):​n.150-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,188 control chromosomes in the GnomAD database, including 2,782 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 0.17 (2782 hom., cov: 32)
• Consequence: ENSG00000303737 ENST00000796848.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 17 publications found

Genes affected

ENSG00000303737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796848.1. 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
	ENSG00000303737	ENST00000796848.1		n.150-68G>A		intron	N/A
	ENSG00000303737	ENST00000796849.1		n.110+26185G>A		intron	N/A
	ENSG00000303737	ENST00000796850.1		n.72-68G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25280 AN: 152070 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.166 AC: 25295 AN: 152188 Hom.: 2782 Cov.: 32 AF XY: 0.175 AC XY: 13053 AN XY: 74412

African (AFR) AF: 0.0703 AC: 2919 AN: 41540

American (AMR) AF: 0.315 AC: 4813 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2119 AN: 5176

South Asian (SAS) AF: 0.199 AC: 957 AN: 4808

European-Finnish (FIN) AF: 0.245 AC: 2594 AN: 10584

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10567 AN: 68002

Other (OTH) AF: 0.197 AC: 417 AN: 2114

Alfa AF: 0.165 Hom.: 10108

Bravo AF: 0.168

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.28
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4667682; hg19: chr2-172127920; COSMIC: COSV69716549;