rs1815686

Variant names:

• chr13-105457135-C-G
• rs1815686

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 0.511 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.438 AC: 17731 AN: 40496

American (AMR) AF: 0.524 AC: 7821 AN: 14914

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1938 AN: 3456

East Asian (EAS) AF: 0.302 AC: 1470 AN: 4864

South Asian (SAS) AF: 0.488 AC: 2289 AN: 4686

European-Finnish (FIN) AF: 0.539 AC: 5216 AN: 9678

Middle Eastern (MID) AF: 0.554 AC: 154 AN: 278

European-Non Finnish (NFE) AF: 0.561 AC: 37829 AN: 67444

Other (OTH) AF: 0.530 AC: 1081 AN: 2040

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1815686; hg19: chr13-106109484;