17-61419288-T-C

Position:

• chr17-61419288-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 0.61 in 151,834 control chromosomes in the GnomAD database, including 29,021 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 (29021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.610 AC: 92613 AN: 151718 Hom.: 28996 Cov.: 31

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.610 AC: 92686 AN: 151834 Hom.: 29021 Cov.: 31 AF XY: 0.618 AC XY: 45819 AN XY: 74194

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.611

Alfa AF: 0.628 Hom.: 16126

Bravo AF: 0.595

Asia WGS AF: 0.590 AC: 2057 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	1.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2079795; hg19: chr17-59496649;