chr2-171661641-A-G

Variant names:

• chr2-171661641-A-G
• rs6433309

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 0.815 in 152,236 control chromosomes in the GnomAD database, including 50,806 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 0.82 (50806 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.815 AC: 124034 AN: 152118 Hom.: 50757 Cov.: 34

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.815 AC: 124139 AN: 152236 Hom.: 50806 Cov.: 34 AF XY: 0.815 AC XY: 60678 AN XY: 74428

African (AFR) AF: 0.764 AC: 31714 AN: 41508

American (AMR) AF: 0.843 AC: 12889 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2469 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4479 AN: 5188

South Asian (SAS) AF: 0.812 AC: 3918 AN: 4824

European-Finnish (FIN) AF: 0.868 AC: 9202 AN: 10604

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56757 AN: 68024

Other (OTH) AF: 0.804 AC: 1699 AN: 2114

Alfa AF: 0.824 Hom.: 26405

Bravo AF: 0.808

Asia WGS AF: 0.854 AC: 2972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6433309; hg19: chr2-172518151;