rs17348849

Variant names:

• chr2-14572602-T-A
• rs17348849

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 0.135 in 152,252 control chromosomes in the GnomAD database, including 1,825 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 0.13 (1825 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 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: 0.135 AC: 20506 AN: 152134 Hom.: 1825 Cov.: 33

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0853

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.135 AC: 20512 AN: 152252 Hom.: 1825 Cov.: 33 AF XY: 0.138 AC XY: 10272 AN XY: 74432

African (AFR) AF: 0.0341 AC: 1418 AN: 41564

American (AMR) AF: 0.147 AC: 2252 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.0855 AC: 442 AN: 5168

South Asian (SAS) AF: 0.249 AC: 1205 AN: 4830

European-Finnish (FIN) AF: 0.236 AC: 2502 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11787 AN: 68014

Other (OTH) AF: 0.122 AC: 258 AN: 2116

Alfa AF: 0.149 Hom.: 251

Bravo AF: 0.121

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.063
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17348849; hg19: chr2-14712726;