13-89911624-T-C

Variant names:

• chr13-89911624-T-C
• rs9522789

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 0.273 in 152,034 control chromosomes in the GnomAD database, including 6,355 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 0.27 (6355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• 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 (AMR) allele frequency at 95% confidence interval = 0.394 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: 0.273 AC: 41488 AN: 151916 Hom.: 6334 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.273 AC: 41528 AN: 152034 Hom.: 6355 Cov.: 32 AF XY: 0.274 AC XY: 20351 AN XY: 74310

African (AFR) AF: 0.147 AC: 6101 AN: 41468

American (AMR) AF: 0.402 AC: 6143 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1326 AN: 5172

South Asian (SAS) AF: 0.246 AC: 1188 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21083 AN: 67960

Other (OTH) AF: 0.297 AC: 624 AN: 2104

Alfa AF: 0.219 Hom.: 698

Bravo AF: 0.283

Asia WGS AF: 0.215 AC: 749 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	3.4
DANN	Benign	0.61
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs9522789; hg19: chr13-90563878;