rs17048175

Variant names:

• chr2-114156886-T-C
• rs17048175

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.189 in 152,192 control chromosomes in the GnomAD database, including 3,892 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 0.19 (3892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.189 AC: 28735 AN: 152074 Hom.: 3868 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.189 AC: 28810 AN: 152192 Hom.: 3892 Cov.: 33 AF XY: 0.189 AC XY: 14040 AN XY: 74426

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0990 Hom.: 209

Bravo AF: 0.202

Asia WGS AF: 0.161 AC: 562 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	4.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17048175; hg19: chr2-114914463;