chr2-60213064-G-C

Variant names:

• chr2-60213064-G-C
• rs11125832

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 0.388 in 151,934 control chromosomes in the GnomAD database, including 12,266 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 0.39 (12266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.388 AC: 58941 AN: 151814 Hom.: 12259 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.388 AC: 58977 AN: 151934 Hom.: 12266 Cov.: 32 AF XY: 0.391 AC XY: 28991 AN XY: 74236

African (AFR) AF: 0.237 AC: 9821 AN: 41420

American (AMR) AF: 0.456 AC: 6967 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1308 AN: 3464

East Asian (EAS) AF: 0.471 AC: 2433 AN: 5166

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4810

European-Finnish (FIN) AF: 0.463 AC: 4870 AN: 10516

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30333 AN: 67954

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.262 Hom.: 652

Bravo AF: 0.391

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.54
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs11125832; hg19: chr2-60440199;