rs3760399

Variant names:

• chr17-34253539-A-G
• rs3760399

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 0.0433 in 152,184 control chromosomes in the GnomAD database, including 275 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 0.043 (275 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6584 AN: 152066 Hom.: 272 Cov.: 33

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0934

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0433 AC: 6593 AN: 152184 Hom.: 275 Cov.: 33 AF XY: 0.0469 AC XY: 3486 AN XY: 74396

African (AFR) AF: 0.0106 AC: 440 AN: 41546

American (AMR) AF: 0.0417 AC: 638 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.0936 AC: 484 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4824

European-Finnish (FIN) AF: 0.0525 AC: 555 AN: 10574

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3125 AN: 67996

Other (OTH) AF: 0.0489 AC: 103 AN: 2106

Alfa AF: 0.0437 Hom.: 33

Bravo AF: 0.0372

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.033
DANN	Benign	0.33
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3760399; hg19: chr17-32580558;