rs2168993

Variant names:

• chr5-116999124-C-G
• rs2168993

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 0.563 in 151,934 control chromosomes in the GnomAD database, including 26,048 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 0.56 (26048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.563 AC: 85407 AN: 151816 Hom.: 26007 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.563 AC: 85509 AN: 151934 Hom.: 26048 Cov.: 32 AF XY: 0.555 AC XY: 41197 AN XY: 74240

African (AFR) AF: 0.808 AC: 33533 AN: 41512

American (AMR) AF: 0.505 AC: 7715 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2171 AN: 5174

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4147 AN: 10500

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32172 AN: 67878

Other (OTH) AF: 0.545 AC: 1148 AN: 2106

Alfa AF: 0.525 Hom.: 3071

Bravo AF: 0.582

Asia WGS AF: 0.415 AC: 1438 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.20
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2168993; hg19: chr5-116334820; COSMIC: COSV50463295;