17-61414907-A-T

Variant names:

• chr17-61414907-A-T
• rs758599

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 0.609 in 152,154 control chromosomes in the GnomAD database, including 28,899 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 (28899 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.609 AC: 92574 AN: 152036 Hom.: 28874 Cov.: 34

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.609 AC: 92641 AN: 152154 Hom.: 28899 Cov.: 34 AF XY: 0.615 AC XY: 45758 AN XY: 74404

African (AFR) AF: 0.466 AC: 19349 AN: 41484

American (AMR) AF: 0.616 AC: 9426 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3368 AN: 5184

South Asian (SAS) AF: 0.609 AC: 2939 AN: 4824

European-Finnish (FIN) AF: 0.736 AC: 7791 AN: 10588

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45218 AN: 67992

Other (OTH) AF: 0.617 AC: 1303 AN: 2112

Alfa AF: 0.641 Hom.: 3929

Bravo AF: 0.595

Asia WGS AF: 0.594 AC: 2067 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	2.1
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs758599; hg19: chr17-59492268;