chr13-88716410-C-A

Variant names:

• chr13-88716410-C-A
• rs9559892

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 0.115 in 151,904 control chromosomes in the GnomAD database, including 1,628 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 (1628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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: 0.115 AC: 17481 AN: 151786 Hom.: 1619 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.115 AC: 17513 AN: 151904 Hom.: 1628 Cov.: 32 AF XY: 0.119 AC XY: 8830 AN XY: 74254

African (AFR) AF: 0.242 AC: 10006 AN: 41392

American (AMR) AF: 0.0595 AC: 908 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1315 AN: 5140

South Asian (SAS) AF: 0.136 AC: 654 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1193 AN: 10542

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0413 AC: 2807 AN: 67956

Other (OTH) AF: 0.106 AC: 223 AN: 2108

Alfa AF: 0.0887 Hom.: 130

Bravo AF: 0.118

Asia WGS AF: 0.177 AC: 610 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.51
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9559892; hg19: chr13-89368664;