rs2176040

Variant names:

• chr2-226228086-A-G
• rs2176040

Your query was ambiguous. Multiple possible variants found:

• chr2-226228086-A-G
• chr2-226228086-A-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 0.678 in 151,984 control chromosomes in the GnomAD database, including 35,230 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 0.68 (35230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 66 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102993 AN: 151864 Hom.: 35192 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.678 AC: 103085 AN: 151984 Hom.: 35230 Cov.: 31 AF XY: 0.679 AC XY: 50457 AN XY: 74270

African (AFR) AF: 0.693 AC: 28718 AN: 41450

American (AMR) AF: 0.740 AC: 11300 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4782 AN: 5158

South Asian (SAS) AF: 0.763 AC: 3668 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6617 AN: 10560

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43436 AN: 67954

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.656 Hom.: 45386

Bravo AF: 0.688

Asia WGS AF: 0.846 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.7
DANN	Benign	0.80
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2176040; hg19: chr2-227092802;