chr2-218113757-A-C

Variant names:

• chr2-218113757-A-C
• rs6759893

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 0.635 in 152,152 control chromosomes in the GnomAD database, including 33,166 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 0.64 (33166 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 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: 0.635 AC: 96517 AN: 152034 Hom.: 33103 Cov.: 33

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.635 AC: 96628 AN: 152152 Hom.: 33166 Cov.: 33 AF XY: 0.630 AC XY: 46809 AN XY: 74350

African (AFR) AF: 0.909 AC: 37760 AN: 41528

American (AMR) AF: 0.578 AC: 8842 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3468

East Asian (EAS) AF: 0.360 AC: 1855 AN: 5158

South Asian (SAS) AF: 0.608 AC: 2934 AN: 4828

European-Finnish (FIN) AF: 0.431 AC: 4559 AN: 10578

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36145 AN: 67992

Other (OTH) AF: 0.649 AC: 1371 AN: 2112

Alfa AF: 0.593 Hom.: 3506

Bravo AF: 0.654

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6759893; hg19: chr2-218978480;