rs252952

chr5-161287327-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.305

Alfa AF: 0.292 Hom.: 1291

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs252952; hg19: chr5-160714334;