rs17412774

Variant names:

• chr2-146016380-A-C
• rs17412774

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 0.336 in 151,968 control chromosomes in the GnomAD database, including 10,593 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 0.34 (10593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 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: 0.336 AC: 51042 AN: 151850 Hom.: 10597 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.336 AC: 51034 AN: 151968 Hom.: 10593 Cov.: 32 AF XY: 0.336 AC XY: 24961 AN XY: 74248

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.358

Alfa AF: 0.375 Hom.: 1470

Bravo AF: 0.334

Asia WGS AF: 0.405 AC: 1405 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17412774; hg19: chr2-146773948;