17-56695877-T-G

Variant names:

• chr17-56695877-T-G
• rs227731

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 0.518 in 152,074 control chromosomes in the GnomAD database, including 21,995 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 0.52 (21995 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.518 AC: 78642 AN: 151956 Hom.: 21948 Cov.: 33

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.518 AC: 78740 AN: 152074 Hom.: 21995 Cov.: 33 AF XY: 0.511 AC XY: 38024 AN XY: 74352

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.462

Alfa AF: 0.434 Hom.: 31269

Bravo AF: 0.518

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227731; hg19: chr17-54773238;