chr17-34373905-A-G

Variant names:

• chr17-34373905-A-G
• rs159290

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 0.415 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.300 AC: 12445 AN: 41480

American (AMR) AF: 0.545 AC: 8328 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1365 AN: 3464

East Asian (EAS) AF: 0.525 AC: 2713 AN: 5168

South Asian (SAS) AF: 0.487 AC: 2347 AN: 4820

European-Finnish (FIN) AF: 0.476 AC: 5016 AN: 10546

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29467 AN: 67992

Other (OTH) AF: 0.420 AC: 889 AN: 2116

Alfa AF: 0.434 Hom.: 5661

Bravo AF: 0.416

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.42
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs159290; hg19: chr17-32700924;