rs12457996

Variant names:

• chr18-43292308-T-C
• rs12457996

Your query was ambiguous. Multiple possible variants found:

• chr18-43292308-T-C
• chr18-43292308-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.188 in 152,036 control chromosomes in the GnomAD database, including 2,898 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 0.19 (2898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.188 AC: 28617 AN: 151918 Hom.: 2892 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00580

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.188 AC: 28640 AN: 152036 Hom.: 2898 Cov.: 32 AF XY: 0.187 AC XY: 13893 AN XY: 74300

African (AFR) AF: 0.137 AC: 5697 AN: 41496

American (AMR) AF: 0.190 AC: 2905 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3470

East Asian (EAS) AF: 0.00581 AC: 30 AN: 5164

South Asian (SAS) AF: 0.121 AC: 584 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2617 AN: 10554

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15376 AN: 67954

Other (OTH) AF: 0.196 AC: 414 AN: 2112

Alfa AF: 0.207 Hom.: 8292

Bravo AF: 0.184

Asia WGS AF: 0.0700 AC: 244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12457996; hg19: chr18-40872273;