rs690877

Variant names:

• chr2-218857941-T-C
• rs690877

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.805 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

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.785

Alfa AF: 0.759 Hom.: 42635

Bravo AF: 0.812

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs690877; hg19: chr2-219722664;