rs4671826

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000235495 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235495	ENST00000419809.1	n.126+2135G>A		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.457

Alfa AF: 0.494 Hom.: 9126

Bravo AF: 0.445

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4671826; hg19: chr2-67908949;