rs17042407

Variant names:

• chr2-112801337-T-C
• rs17042407

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 0.226 in 152,222 control chromosomes in the GnomAD database, including 4,038 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 0.23 (4038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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: 0.226 AC: 34431 AN: 152104 Hom.: 4038 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.226 AC: 34436 AN: 152222 Hom.: 4038 Cov.: 32 AF XY: 0.222 AC XY: 16512 AN XY: 74442

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.227

Alfa AF: 0.253 Hom.: 10015

Bravo AF: 0.225

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
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: rs17042407; hg19: chr2-113558914;