rs13251447

Positions:

• chr8-6933188-C-A
• chr8-6933188-C-T

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 0.214 in 152,168 control chromosomes in the GnomAD database, including 3,682 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 0.21 (3682 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32586 AN: 152050 Hom.: 3688 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.214 AC: 32576 AN: 152168 Hom.: 3682 Cov.: 33 AF XY: 0.211 AC XY: 15726 AN XY: 74386

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.217

Alfa AF: 0.234 Hom.: 8603

Bravo AF: 0.210

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13251447; hg19: chr8-6790710;