17-56766131-T-C

Variant names:

• chr17-56766131-T-C
• rs17820808

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0635 in 152,150 control chromosomes in the GnomAD database, including 371 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 0.064 (371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 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: 0.0635 AC: 9659 AN: 152032 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0635 AC: 9665 AN: 152150 Hom.: 371 Cov.: 32 AF XY: 0.0652 AC XY: 4852 AN XY: 74384

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0735

Gnomad4 OTH AF: 0.0607

Alfa AF: 0.0697 Hom.: 627

Bravo AF: 0.0651

Asia WGS AF: 0.0630 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17820808; hg19: chr17-54843492;