13-83875389-C-T

Variant names:

• chr13-83875389-C-T
• rs9531520

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 0.147 in 151,782 control chromosomes in the GnomAD database, including 2,011 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 0.15 (2011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 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: 0.148 AC: 22385 AN: 151662 Hom.: 2013 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.147 AC: 22383 AN: 151782 Hom.: 2011 Cov.: 32 AF XY: 0.149 AC XY: 11042 AN XY: 74188

African (AFR) AF: 0.0546 AC: 2265 AN: 41508

American (AMR) AF: 0.170 AC: 2597 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3462

East Asian (EAS) AF: 0.327 AC: 1687 AN: 5160

South Asian (SAS) AF: 0.337 AC: 1627 AN: 4828

European-Finnish (FIN) AF: 0.109 AC: 1153 AN: 10582

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11913 AN: 67678

Other (OTH) AF: 0.167 AC: 351 AN: 2106

Alfa AF: 0.151 Hom.: 333

Bravo AF: 0.146

Asia WGS AF: 0.288 AC: 992 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.24
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9531520; hg19: chr13-84449524;