rs17039430

Variant names:

• chr2-49912348-G-A
• rs17039430

Your query was ambiguous. Multiple possible variants found:

• chr2-49912348-G-A
• chr2-49912348-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 0.146 in 151,772 control chromosomes in the GnomAD database, including 2,078 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 0.15 (2078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 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: 0.146 AC: 22148 AN: 151654 Hom.: 2076 Cov.: 32

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.146 AC: 22147 AN: 151772 Hom.: 2078 Cov.: 32 AF XY: 0.150 AC XY: 11144 AN XY: 74136

African (AFR) AF: 0.0425 AC: 1763 AN: 41462

American (AMR) AF: 0.224 AC: 3403 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1195 AN: 5136

South Asian (SAS) AF: 0.138 AC: 665 AN: 4814

European-Finnish (FIN) AF: 0.239 AC: 2511 AN: 10494

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11447 AN: 67886

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.119 Hom.: 344

Bravo AF: 0.147

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.55
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs17039430; hg19: chr2-50139486;