rs752596

Variant names:

• chr5-170827611-G-A
• rs752596

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 0.43 in 151,154 control chromosomes in the GnomAD database, including 15,762 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 0.43 (15762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

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 (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.430 AC: 64987 AN: 151034 Hom.: 15754 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.430 AC: 64997 AN: 151154 Hom.: 15762 Cov.: 31 AF XY: 0.436 AC XY: 32212 AN XY: 73876

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.476

Alfa AF: 0.485 Hom.: 10779

Bravo AF: 0.423

Asia WGS AF: 0.634 AC: 2205 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	0.56
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752596; hg19: chr5-170254615; COSMIC: COSV60230384;