rs2118732

Variant names:

• chr5-80087453-G-A
• rs2118732

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 0.265 in 151,938 control chromosomes in the GnomAD database, including 7,139 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 0.27 (7139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.265 AC: 40187 AN: 151818 Hom.: 7111 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.265 AC: 40270 AN: 151938 Hom.: 7139 Cov.: 31 AF XY: 0.267 AC XY: 19812 AN XY: 74272

African (AFR) AF: 0.504 AC: 20877 AN: 41430

American (AMR) AF: 0.258 AC: 3941 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3462

East Asian (EAS) AF: 0.255 AC: 1322 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1162 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2071 AN: 10534

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9501 AN: 67936

Other (OTH) AF: 0.260 AC: 550 AN: 2112

Alfa AF: 0.188 Hom.: 8839

Bravo AF: 0.283

Asia WGS AF: 0.303 AC: 1050 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2118732; hg19: chr5-79383276; COSMIC: COSV63468617;