17-34373905-A-G

Variant names:

• chr17-34373905-A-G
• rs159290

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 0.415 in 152,080 control chromosomes in the GnomAD database, including 13,641 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 0.41 (13641 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.535 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: 0.415 AC: 63044 AN: 151962 Hom.: 13625 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.415 AC: 63101 AN: 152080 Hom.: 13641 Cov.: 33 AF XY: 0.421 AC XY: 31283 AN XY: 74300

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.420

Alfa AF: 0.437 Hom.: 3215

Bravo AF: 0.416

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159290; hg19: chr17-32700924;