rs12718890

Positions:

• chr7-54686782-G-A

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 0.452 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.431

Alfa AF: 0.416 Hom.: 10258

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12718890; hg19: chr7-54754475;