rs12953809

Variant names:

• chr18-77246693-C-T
• rs12953809

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 0.0619 in 152,198 control chromosomes in the GnomAD database, including 352 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 0.062 (352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 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: 0.0618 AC: 9399 AN: 152080 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0619 AC: 9418 AN: 152198 Hom.: 352 Cov.: 32 AF XY: 0.0611 AC XY: 4547 AN XY: 74400

Gnomad4 AFR AF: 0.0207

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.0358

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0776 Hom.: 244

Bravo AF: 0.0584

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12953809; hg19: chr18-74958649;