rs690877

Variant names:

• chr2-218857941-T-C
• rs690877

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.805 in 152,186 control chromosomes in the GnomAD database, including 50,119 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 0.81 (50119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122446 AN: 152068 Hom.: 50045 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.805 AC: 122573 AN: 152186 Hom.: 50119 Cov.: 33 AF XY: 0.803 AC XY: 59755 AN XY: 74386

African (AFR) AF: 0.955 AC: 39694 AN: 41550

American (AMR) AF: 0.772 AC: 11811 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2577 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3763 AN: 5164

South Asian (SAS) AF: 0.600 AC: 2890 AN: 4816

European-Finnish (FIN) AF: 0.788 AC: 8346 AN: 10588

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50881 AN: 67986

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.766 Hom.: 64093

Bravo AF: 0.812

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs690877; hg19: chr2-219722664;