rs17412774

Variant names:

• chr2-146016380-A-C
• rs17412774

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0862 AC: 3580 AN: 41514

American (AMR) AF: 0.399 AC: 6078 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3468

East Asian (EAS) AF: 0.637 AC: 3276 AN: 5144

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4822

European-Finnish (FIN) AF: 0.359 AC: 3781 AN: 10546

Middle Eastern (MID) AF: 0.300 AC: 87 AN: 290

European-Non Finnish (NFE) AF: 0.441 AC: 29963 AN: 67924

Other (OTH) AF: 0.358 AC: 754 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.80
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs17412774; hg19: chr2-146773948;