chr17-34259075-C-T

Variant names:

• chr17-34259075-C-T
• rs2530797

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 0.705 in 152,126 control chromosomes in the GnomAD database, including 38,508 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 0.70 (38508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.705 AC: 107116 AN: 152008 Hom.: 38442 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.705 AC: 107248 AN: 152126 Hom.: 38508 Cov.: 32 AF XY: 0.709 AC XY: 52718 AN XY: 74350

African (AFR) AF: 0.843 AC: 35005 AN: 41518

American (AMR) AF: 0.721 AC: 11012 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3802 AN: 5166

South Asian (SAS) AF: 0.760 AC: 3667 AN: 4822

European-Finnish (FIN) AF: 0.671 AC: 7093 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42548 AN: 67986

Other (OTH) AF: 0.670 AC: 1413 AN: 2108

Alfa AF: 0.667 Hom.: 53879

Bravo AF: 0.711

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.011
DANN	Benign	0.56
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2530797; hg19: chr17-32586094;