rs9602859

Variant names:

• chr13-85871859-G-A
• rs9602859

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 0.102 in 151,922 control chromosomes in the GnomAD database, including 1,071 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 0.10 (1071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.101 AC: 15389 AN: 151804 Hom.: 1068 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0635

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0902

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

GnomAD4 genome AF: 0.102 AC: 15426 AN: 151922 Hom.: 1071 Cov.: 32 AF XY: 0.105 AC XY: 7782 AN XY: 74270

African (AFR) AF: 0.198 AC: 8189 AN: 41408

American (AMR) AF: 0.0744 AC: 1136 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0635 AC: 220 AN: 3466

East Asian (EAS) AF: 0.0629 AC: 325 AN: 5170

South Asian (SAS) AF: 0.120 AC: 577 AN: 4800

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10544

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0514 AC: 3491 AN: 67956

Other (OTH) AF: 0.0931 AC: 196 AN: 2106

Alfa AF: 0.0667 Hom.: 238

Bravo AF: 0.102

Asia WGS AF: 0.106 AC: 368 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	0.90
DANN	Benign	0.17
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9602859; hg19: chr13-86445994;