rs13258548

chr8-127484602-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.256

Alfa AF: 0.261 Hom.: 1101

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13258548; hg19: chr8-128496847;