rs2339001

Variant names:

• chr17-34337353-G-A
• rs2339001

Your query was ambiguous. Multiple possible variants found:

• chr17-34337353-G-A
• chr17-34337353-G-T

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 0.163 in 151,836 control chromosomes in the GnomAD database, including 2,495 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 0.16 (2495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.356 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: 0.163 AC: 24712 AN: 151718 Hom.: 2487 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.163 AC: 24749 AN: 151836 Hom.: 2495 Cov.: 32 AF XY: 0.169 AC XY: 12509 AN XY: 74162

African (AFR) AF: 0.0648 AC: 2686 AN: 41442

American (AMR) AF: 0.262 AC: 3995 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1532 AN: 5134

South Asian (SAS) AF: 0.370 AC: 1773 AN: 4792

European-Finnish (FIN) AF: 0.156 AC: 1639 AN: 10536

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11906 AN: 67920

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.0756 Hom.: 109

Bravo AF: 0.165

Asia WGS AF: 0.304 AC: 1054 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	2.3
DANN	Benign	0.58
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2339001; hg19: chr17-32664372;