rs2926832

Variant names:

• chr5-153816112-G-A
• rs2926832

Your query was ambiguous. Multiple possible variants found:

• chr5-153816112-G-A
• chr5-153816112-G-C

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 0.252 in 152,026 control chromosomes in the GnomAD database, including 6,250 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 0.25 (6250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.252 AC: 38275 AN: 151908 Hom.: 6233 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.252 AC: 38333 AN: 152026 Hom.: 6250 Cov.: 32 AF XY: 0.261 AC XY: 19412 AN XY: 74322

African (AFR) AF: 0.283 AC: 11708 AN: 41438

American (AMR) AF: 0.372 AC: 5678 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4381 AN: 5178

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4814

European-Finnish (FIN) AF: 0.203 AC: 2146 AN: 10576

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11489 AN: 67962

Other (OTH) AF: 0.240 AC: 507 AN: 2116

Alfa AF: 0.209 Hom.: 476

Bravo AF: 0.269

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.70
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2926832; hg19: chr5-153195672;