2-169363371-A-G

Variant names:

• chr2-169363371-A-G
• rs3755166

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 0.628 in 152,052 control chromosomes in the GnomAD database, including 30,287 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 0.63 (30287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.628 AC: 95430 AN: 151934 Hom.: 30231 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.628 AC: 95549 AN: 152052 Hom.: 30287 Cov.: 32 AF XY: 0.628 AC XY: 46686 AN XY: 74330

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.636

Alfa AF: 0.605 Hom.: 43032

Bravo AF: 0.634

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755166; hg19: chr2-170219881;