rs752596

Positions:

• chr5-170827611-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;