rs2857654

Variant names:

• chr17-34252512-C-A
• rs2857654

Your query was ambiguous. Multiple possible variants found:

• chr17-34252512-C-A
• chr17-34252512-C-G
• chr17-34252512-C-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;