chr17-34248740-T-C

Variant names:

• chr17-34248740-T-C
• rs2857653

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 0.853 in 152,244 control chromosomes in the GnomAD database, including 55,751 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 0.85 (55751 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 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: 0.853 AC: 129728 AN: 152126 Hom.: 55688 Cov.: 33

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.853 AC: 129851 AN: 152244 Hom.: 55751 Cov.: 33 AF XY: 0.856 AC XY: 63682 AN XY: 74420

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.829

Alfa AF: 0.840 Hom.: 3879

Bravo AF: 0.850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857653; hg19: chr17-32575759;