rs718831

Variant names:

• chr13-106391420-T-C
• rs718831

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 0.477 in 151,752 control chromosomes in the GnomAD database, including 17,412 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 0.48 (17412 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

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 (AMR) allele frequency at 95% confidence interval = 0.504 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: 0.477 AC: 72323 AN: 151634 Hom.: 17395 Cov.: 30

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.477 AC: 72372 AN: 151752 Hom.: 17412 Cov.: 30 AF XY: 0.477 AC XY: 35400 AN XY: 74158

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.461

Alfa AF: 0.468 Hom.: 8076

Bravo AF: 0.475

Asia WGS AF: 0.347 AC: 1209 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	0.94
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718831; hg19: chr13-107043768;