rs1359387

Positions:

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

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 0.384 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.382

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359387; hg19: chr13-106072135;