17-56627677-C-T

Position:

• chr17-56627677-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 0.0182 in 152,194 control chromosomes in the GnomAD database, including 61 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 0.018 (61 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0182 AC: 2768 AN: 152076 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00727

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0221

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00412

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0182 AC: 2767 AN: 152194 Hom.: 61 Cov.: 32 AF XY: 0.0197 AC XY: 1468 AN XY: 74390

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.00726

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.00412

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.00901 Hom.: 6

Bravo AF: 0.0178

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491160; hg19: chr17-54705038;