chr2-165402907-C-G

Variant names:

• chr2-165402907-C-G
• rs2082366

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 0.681 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.774 AC: 32087 AN: 41456

American (AMR) AF: 0.600 AC: 9136 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2475 AN: 3464

East Asian (EAS) AF: 0.692 AC: 3561 AN: 5148

South Asian (SAS) AF: 0.744 AC: 3575 AN: 4808

European-Finnish (FIN) AF: 0.615 AC: 6482 AN: 10544

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 43995 AN: 67924

Other (OTH) AF: 0.662 AC: 1394 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.26
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2082366; hg19: chr2-166259417;