rs252952

Variant names:

• chr5-161287327-T-G
• rs252952

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 0.288 in 152,132 control chromosomes in the GnomAD database, including 7,100 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 0.29 (7100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 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: 0.288 AC: 43732 AN: 152014 Hom.: 7095 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.288 AC: 43761 AN: 152132 Hom.: 7100 Cov.: 32 AF XY: 0.286 AC XY: 21277 AN XY: 74362

African (AFR) AF: 0.430 AC: 17847 AN: 41480

American (AMR) AF: 0.324 AC: 4957 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5190

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2463 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15435 AN: 68004

Other (OTH) AF: 0.305 AC: 643 AN: 2108

Alfa AF: 0.296 Hom.: 1367

Bravo AF: 0.302

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.50
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs252952; hg19: chr5-160714334;