rs17659543

Variant names:

• chr2-112958729-C-T
• rs17659543

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 0.164 in 152,096 control chromosomes in the GnomAD database, including 2,234 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 (2234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.164 AC: 24978 AN: 151978 Hom.: 2231 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.164 AC: 24987 AN: 152096 Hom.: 2234 Cov.: 32 AF XY: 0.158 AC XY: 11730 AN XY: 74362

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.168

Alfa AF: 0.158 Hom.: 1080

Bravo AF: 0.171

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17659543; hg19: chr2-113716306;