chr2-67681817-C-T

Variant names:

• chr2-67681817-C-T
• rs4671826
• ENST00000419809.1:n.126+2135G>A

Variant summary

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

The ENST00000419809.1(ENSG00000235495):​n.126+2135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,880 control chromosomes in the GnomAD database, including 15,955 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 0.45 (15955 hom., cov: 31)
• Consequence: ENSG00000235495 ENST00000419809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 5 publications found

Genes affected

ENSG00000235495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419809.1. 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
	ENSG00000235495	ENST00000419809.1	TSL:3	n.126+2135G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67718 AN: 151762 Hom.: 15942 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.446 AC: 67762 AN: 151880 Hom.: 15955 Cov.: 31 AF XY: 0.445 AC XY: 33041 AN XY: 74208

African (AFR) AF: 0.314 AC: 13006 AN: 41428

American (AMR) AF: 0.541 AC: 8248 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5164

South Asian (SAS) AF: 0.486 AC: 2335 AN: 4802

European-Finnish (FIN) AF: 0.480 AC: 5061 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34494 AN: 67916

Other (OTH) AF: 0.457 AC: 962 AN: 2106

Alfa AF: 0.492 Hom.: 10107

Bravo AF: 0.445

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.24
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4671826; hg19: chr2-67908949;