rs13248165

Variant names:

• chr8-56280283-T-A
• rs13248165

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 0.155 in 152,206 control chromosomes in the GnomAD database, including 1,875 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 0.16 (1875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.155 AC: 23609 AN: 152088 Hom.: 1872 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.155 AC: 23624 AN: 152206 Hom.: 1875 Cov.: 32 AF XY: 0.153 AC XY: 11407 AN XY: 74418

African (AFR) AF: 0.200 AC: 8308 AN: 41508

American (AMR) AF: 0.161 AC: 2461 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.0601 AC: 312 AN: 5194

South Asian (SAS) AF: 0.136 AC: 658 AN: 4828

European-Finnish (FIN) AF: 0.133 AC: 1412 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9282 AN: 67998

Other (OTH) AF: 0.173 AC: 364 AN: 2110

Alfa AF: 0.148 Hom.: 199

Bravo AF: 0.160

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs13248165; hg19: chr8-57192842;