17-63500687-T-C

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 0.615 in 151,822 control chromosomes in the GnomAD database, including 30,235 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 0.61 (30235 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

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 = 0.83 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: 0.614 AC: 93181 AN: 151704 Hom.: 30148 Cov.: 30

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.615 AC: 93330 AN: 151822 Hom.: 30235 Cov.: 30 AF XY: 0.613 AC XY: 45461 AN XY: 74168

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.555

Alfa AF: 0.527 Hom.: 31165

Bravo AF: 0.627

Asia WGS AF: 0.691 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4461142; hg19: chr17-61578048;