2-165402907-C-G

Variant names:

• chr2-165402907-C-G
• rs2082366

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 0.681 in 151,890 control chromosomes in the GnomAD database, including 35,591 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 (35591 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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: 0.681 AC: 103417 AN: 151772 Hom.: 35561 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.681 AC: 103491 AN: 151890 Hom.: 35591 Cov.: 30 AF XY: 0.678 AC XY: 50355 AN XY: 74220

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.662

Alfa AF: 0.534 Hom.: 1381

Bravo AF: 0.682

Asia WGS AF: 0.705 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2082366; hg19: chr2-166259417;