rs2857654

chr17-34252512-C-Achr17-34252512-C-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 0.334 in 152,076 control chromosomes in the GnomAD database, including 9,011 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 0.33 (9011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.334 AC: 50752 AN: 151958 Hom.: 8991 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.334 AC: 50805 AN: 152076 Hom.: 9011 Cov.: 33 AF XY: 0.340 AC XY: 25312 AN XY: 74348

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.319

Alfa AF: 0.0793 Hom.: 86

Bravo AF: 0.344

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.7
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857654; hg19: chr17-32579531;