rs1359387

Variant names:

• chr13-105419786-G-A
• rs1359387

Your query was ambiguous. Multiple possible variants found:

• chr13-105419786-G-A
• chr13-105419786-G-C

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 0.384 in 151,876 control chromosomes in the GnomAD database, including 11,691 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 0.38 (11691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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: 0.384 AC: 58337 AN: 151758 Hom.: 11684 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.384 AC: 58369 AN: 151876 Hom.: 11691 Cov.: 32 AF XY: 0.381 AC XY: 28290 AN XY: 74220

African (AFR) AF: 0.306 AC: 12669 AN: 41400

American (AMR) AF: 0.467 AC: 7131 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3260 AN: 5152

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3334 AN: 10560

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27981 AN: 67906

Other (OTH) AF: 0.382 AC: 804 AN: 2106

Alfa AF: 0.255 Hom.: 629

Bravo AF: 0.395

Asia WGS AF: 0.465 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1359387; hg19: chr13-106072135;