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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.671

Alfa AF: 0.656 Hom.: 4906

Bravo AF: 0.688

Asia WGS AF: 0.846 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2176040; hg19: chr2-227092802;