rs17451107

Variant names:

• chr3-157079820-T-C
• rs17451107

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 0.382 in 151,932 control chromosomes in the GnomAD database, including 11,306 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 0.38 (11306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.382 AC: 57941 AN: 151814 Hom.: 11305 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.382 AC: 57974 AN: 151932 Hom.: 11306 Cov.: 32 AF XY: 0.376 AC XY: 27946 AN XY: 74272

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.416

Alfa AF: 0.406 Hom.: 20659

Bravo AF: 0.392

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17451107; hg19: chr3-156797609;