rs13258548

Variant names:

• chr8-127484602-A-G
• rs13258548

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 0.245 in 152,012 control chromosomes in the GnomAD database, including 5,212 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 0.25 (5212 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 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: 0.245 AC: 37254 AN: 151894 Hom.: 5209 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.245 AC: 37266 AN: 152012 Hom.: 5212 Cov.: 31 AF XY: 0.243 AC XY: 18076 AN XY: 74292

African (AFR) AF: 0.122 AC: 5067 AN: 41484

American (AMR) AF: 0.265 AC: 4054 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3466

East Asian (EAS) AF: 0.120 AC: 622 AN: 5166

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2293 AN: 10530

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22000 AN: 67946

Other (OTH) AF: 0.256 AC: 540 AN: 2108

Alfa AF: 0.254 Hom.: 1235

Bravo AF: 0.239

Asia WGS AF: 0.198 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs13258548; hg19: chr8-128496847;