rs718802

Variant names:

• chr12-113019812-C-A
• rs718802

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 0.127 in 152,144 control chromosomes in the GnomAD database, including 3,495 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 0.13 (3495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.126 AC: 19204 AN: 152026 Hom.: 3483 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.127 AC: 19268 AN: 152144 Hom.: 3495 Cov.: 32 AF XY: 0.123 AC XY: 9142 AN XY: 74418

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.0923 Hom.: 294

Bravo AF: 0.143

Asia WGS AF: 0.0750 AC: 262 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	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718802; hg19: chr12-113457617;