rs2046006

Variant names:

• chr15-94694732-C-A
• rs2046006

Your query was ambiguous. Multiple possible variants found:

• chr15-94694732-C-A
• chr15-94694732-C-T

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 0.31 in 152,082 control chromosomes in the GnomAD database, including 7,926 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 0.31 (7926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 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: 0.311 AC: 47201 AN: 151964 Hom.: 7930 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.310 AC: 47199 AN: 152082 Hom.: 7926 Cov.: 32 AF XY: 0.312 AC XY: 23164 AN XY: 74330

African (AFR) AF: 0.191 AC: 7918 AN: 41498

American (AMR) AF: 0.440 AC: 6720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1968 AN: 5174

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4826

European-Finnish (FIN) AF: 0.304 AC: 3210 AN: 10544

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23282 AN: 67986

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.315 Hom.: 4523

Bravo AF: 0.318

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2046006; hg19: chr15-95237961;