chr2-171661641-A-G

Variant names:

• chr2-171661641-A-G
• rs6433309

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 0.815 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.804

Alfa AF: 0.824 Hom.: 23784

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6433309; hg19: chr2-172518151;