rs718831

Variant names:

• chr13-106391420-T-C
• rs718831

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 0.477 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.484 AC: 20039 AN: 41374

American (AMR) AF: 0.513 AC: 7828 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2069 AN: 5150

South Asian (SAS) AF: 0.355 AC: 1702 AN: 4794

European-Finnish (FIN) AF: 0.539 AC: 5671 AN: 10512

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32320 AN: 67900

Other (OTH) AF: 0.461 AC: 969 AN: 2104

Alfa AF: 0.468 Hom.: 8992

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs718831; hg19: chr13-107043768;