13-48713188-T-A

Variant names:

• chr13-48713188-T-A
• rs9568087

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 0.236 in 152,162 control chromosomes in the GnomAD database, including 5,241 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 0.24 (5241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.236 AC: 35876 AN: 152044 Hom.: 5244 Cov.: 32

Gnomad AFR AF: 0.0620

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.236 AC: 35872 AN: 152162 Hom.: 5241 Cov.: 32 AF XY: 0.244 AC XY: 18160 AN XY: 74382

African (AFR) AF: 0.0620 AC: 2577 AN: 41542

American (AMR) AF: 0.258 AC: 3939 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2285 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4818

European-Finnish (FIN) AF: 0.350 AC: 3697 AN: 10572

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19786 AN: 67988

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.264 Hom.: 732

Bravo AF: 0.222

Asia WGS AF: 0.337 AC: 1174 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	0.24
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9568087; hg19: chr13-49287324;