rs1815686

chr13-105457135-C-G

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 0.511 in 148,758 control chromosomes in the GnomAD database, including 19,607 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 0.51 (19607 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.511 AC: 75983 AN: 148658 Hom.: 19606 Cov.: 25

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.511 AC: 76010 AN: 148758 Hom.: 19607 Cov.: 25 AF XY: 0.508 AC XY: 36774 AN XY: 72320

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.530

Alfa AF: 0.526 Hom.: 2699

Bravo AF: 0.505

Asia WGS AF: 0.429 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1815686; hg19: chr13-106109484;