rs1718377

Variant names:

• chr12-114586432-A-G
• rs1718377

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 0.866 in 152,080 control chromosomes in the GnomAD database, including 58,167 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 0.87 (58167 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.866 AC: 131581 AN: 151962 Hom.: 58123 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.866 AC: 131685 AN: 152080 Hom.: 58167 Cov.: 31 AF XY: 0.871 AC XY: 64743 AN XY: 74364

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.899

Alfa AF: 0.921 Hom.: 89389

Bravo AF: 0.855

Asia WGS AF: 0.950 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1718377; hg19: chr12-115024237;