17-34377773-A-T

Position:

• chr17-34377773-A-T

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 0.743 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.34377773A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.772

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159294; hg19: chr17-32704792;