17-56603681-C-T

Variant names:

• chr17-56603681-C-T
• rs1372857

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 0.504 in 151,952 control chromosomes in the GnomAD database, including 20,999 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 0.50 (20999 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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: 0.504 AC: 76519 AN: 151834 Hom.: 21003 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.504 AC: 76531 AN: 151952 Hom.: 20999 Cov.: 31 AF XY: 0.511 AC XY: 37978 AN XY: 74280

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.535

Alfa AF: 0.574 Hom.: 50830

Bravo AF: 0.492

Asia WGS AF: 0.662 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372857; hg19: chr17-54681042;