17-61419288-T-C

Variant names:

• chr17-61419288-T-C
• rs2079795

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 54 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.465 AC: 19246 AN: 41372

American (AMR) AF: 0.617 AC: 9400 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3337 AN: 5134

South Asian (SAS) AF: 0.622 AC: 2988 AN: 4806

European-Finnish (FIN) AF: 0.753 AC: 7933 AN: 10540

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45251 AN: 67954

Other (OTH) AF: 0.611 AC: 1288 AN: 2108

Alfa AF: 0.627 Hom.: 24391

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2079795; hg19: chr17-59496649;