chr17-61417213-C-T

Position:

• chr17-61417213-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 0.611 in 152,166 control chromosomes in the GnomAD database, including 29,073 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 (29073 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92977 AN: 152046 Hom.: 29047 Cov.: 34

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.611 AC: 93043 AN: 152166 Hom.: 29073 Cov.: 34 AF XY: 0.617 AC XY: 45953 AN XY: 74418

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.615

Alfa AF: 0.648 Hom.: 40225

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs882367; hg19: chr17-59494574;