17-34377773-A-T

Variant names:

• chr17-34377773-A-T
• rs159294

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 0.743 in 152,078 control chromosomes in the GnomAD database, including 44,503 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 0.74 (44503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 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: 0.743 AC: 112907 AN: 151960 Hom.: 44484 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.743 AC: 112975 AN: 152078 Hom.: 44503 Cov.: 32 AF XY: 0.745 AC XY: 55405 AN XY: 74332

African (AFR) AF: 0.457 AC: 18916 AN: 41412

American (AMR) AF: 0.773 AC: 11817 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3051 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4180 AN: 5180

South Asian (SAS) AF: 0.829 AC: 3988 AN: 4812

European-Finnish (FIN) AF: 0.857 AC: 9079 AN: 10600

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59278 AN: 68012

Other (OTH) AF: 0.772 AC: 1628 AN: 2108

Alfa AF: 0.797 Hom.: 6206

Bravo AF: 0.723

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.48
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs159294; hg19: chr17-32704792;