rs2813746

Variant names:

• chr1-90074206-C-A
• rs2813746

Your query was ambiguous. Multiple possible variants found:

• chr1-90074206-C-A
• chr1-90074206-C-T

Variant summary

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

The variant allele was found at a frequency of 0.406 in 152,004 control chromosomes in the GnomAD database, including 13,498 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 0.41 (13498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61736 AN: 151886 Hom.: 13491 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.406 AC: 61752 AN: 152004 Hom.: 13498 Cov.: 32 AF XY: 0.414 AC XY: 30746 AN XY: 74302

African (AFR) AF: 0.242 AC: 10019 AN: 41462

American (AMR) AF: 0.490 AC: 7488 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3466

East Asian (EAS) AF: 0.631 AC: 3254 AN: 5158

South Asian (SAS) AF: 0.558 AC: 2686 AN: 4816

European-Finnish (FIN) AF: 0.466 AC: 4923 AN: 10564

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30258 AN: 67946

Other (OTH) AF: 0.397 AC: 837 AN: 2110

Alfa AF: 0.438 Hom.: 67773

Bravo AF: 0.401

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2813746; hg19: chr1-90539764;