rs1401838

Variant names:

• chr2-76406014-A-G
• rs1401838
• ENST00000798785.1:n.108-3441A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-76406014-A-G
• chr2-76406014-A-T

Variant summary

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

The ENST00000798785.1(ENSG00000287172):​n.108-3441A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,910 control chromosomes in the GnomAD database, including 9,199 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 0.34 (9199 hom., cov: 32)
• Consequence: ENSG00000287172 ENST00000798785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 1 publications found

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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
ENSG00000287172	ENST00000798785.1	n.108-3441A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51017 AN: 151790 Hom.: 9202 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.336 AC: 51034 AN: 151910 Hom.: 9199 Cov.: 32 AF XY: 0.343 AC XY: 25457 AN XY: 74250

African (AFR) AF: 0.207 AC: 8595 AN: 41456

American (AMR) AF: 0.421 AC: 6433 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3466

East Asian (EAS) AF: 0.545 AC: 2794 AN: 5126

South Asian (SAS) AF: 0.332 AC: 1596 AN: 4810

European-Finnish (FIN) AF: 0.433 AC: 4560 AN: 10528

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24175 AN: 67934

Other (OTH) AF: 0.372 AC: 781 AN: 2100

Alfa AF: 0.346 Hom.: 22599

Bravo AF: 0.333

Asia WGS AF: 0.422 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.93
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1401838; hg19: chr2-76633140;