chr17-52995552-A-C

Position:

• chr17-52995552-A-C

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 0.386 in 152,094 control chromosomes in the GnomAD database, including 12,884 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 0.39 (12884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.386 AC: 58635 AN: 151974 Hom.: 12884 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58638 AN: 152094 Hom.: 12884 Cov.: 32 AF XY: 0.388 AC XY: 28814 AN XY: 74322

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.398

Alfa AF: 0.448 Hom.: 10241

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	17
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512855; hg19: chr17-51072912;