rs12452959

Variant names:

• chr17-66208946-A-C
• rs12452959

Your query was ambiguous. Multiple possible variants found:

• chr17-66208946-A-C
• chr17-66208946-A-G
• chr17-66208946-A-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 0.184 in 152,118 control chromosomes in the GnomAD database, including 3,608 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 0.18 (3608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.184 AC: 27893 AN: 152000 Hom.: 3594 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.184 AC: 27939 AN: 152118 Hom.: 3608 Cov.: 32 AF XY: 0.195 AC XY: 14499 AN XY: 74372

African (AFR) AF: 0.109 AC: 4525 AN: 41524

American (AMR) AF: 0.293 AC: 4480 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3649 AN: 5164

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2024 AN: 10572

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10649 AN: 67972

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.172 Hom.: 519

Bravo AF: 0.185

Asia WGS AF: 0.463 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.82
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12452959; hg19: chr17-64205064;