rs12718890

Variant names:

• chr7-54686782-G-A
• rs12718890

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 0.452 in 152,014 control chromosomes in the GnomAD database, including 16,006 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 0.45 (16006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.452 AC: 68717 AN: 151896 Hom.: 15993 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.452 AC: 68766 AN: 152014 Hom.: 16006 Cov.: 32 AF XY: 0.451 AC XY: 33522 AN XY: 74280

African (AFR) AF: 0.572 AC: 23721 AN: 41472

American (AMR) AF: 0.353 AC: 5384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1805 AN: 5172

South Asian (SAS) AF: 0.462 AC: 2223 AN: 4814

European-Finnish (FIN) AF: 0.498 AC: 5245 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27293 AN: 67962

Other (OTH) AF: 0.431 AC: 910 AN: 2112

Alfa AF: 0.418 Hom.: 14054

Bravo AF: 0.447

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.32
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs12718890; hg19: chr7-54754475;