17-39900944-G-A

Variant names:

• chr17-39900944-G-A
• rs8069176

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 0.411 in 151,710 control chromosomes in the GnomAD database, including 13,045 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 (13045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.411 AC: 62257 AN: 151594 Hom.: 13030 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.411 AC: 62321 AN: 151710 Hom.: 13045 Cov.: 32 AF XY: 0.413 AC XY: 30618 AN XY: 74140

African (AFR) AF: 0.351 AC: 14550 AN: 41416

American (AMR) AF: 0.395 AC: 6032 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1425 AN: 3462

East Asian (EAS) AF: 0.270 AC: 1395 AN: 5166

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4826

European-Finnish (FIN) AF: 0.517 AC: 5402 AN: 10446

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.445 AC: 30200 AN: 67830

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.421 Hom.: 20157

Bravo AF: 0.393

Asia WGS AF: 0.375 AC: 1303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs8069176; hg19: chr17-38057197;