rs1535989

Positions:

• chr13-105370372-A-G
• chr13-105370372-A-T

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 0.118 in 152,206 control chromosomes in the GnomAD database, including 1,156 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 0.12 (1156 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105370372A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17874 AN: 152088 Hom.: 1148 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.118 AC: 17899 AN: 152206 Hom.: 1156 Cov.: 32 AF XY: 0.115 AC XY: 8591 AN XY: 74420

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0637

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.106

Alfa AF: 0.100 Hom.: 991

Bravo AF: 0.114

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535989; hg19: chr13-106022722;