rs1535989

Variant names:

• chr13-105370372-A-G
• rs1535989

Your query was ambiguous. Multiple possible variants found:

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

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 0.118 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.163 AC: 6769 AN: 41516

American (AMR) AF: 0.0637 AC: 975 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5172

South Asian (SAS) AF: 0.110 AC: 530 AN: 4832

European-Finnish (FIN) AF: 0.121 AC: 1283 AN: 10604

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7493 AN: 67998

Other (OTH) AF: 0.106 AC: 224 AN: 2114

Alfa AF: 0.103 Hom.: 1295

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1535989; hg19: chr13-106022722;