rs1013209

Positions:

• chr8-24258791-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 0.275 in 151,862 control chromosomes in the GnomAD database, including 5,978 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 0.28 (5978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

ACMG classification

Verdict is Benign. Variant got -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 = 0.325 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: 0.275 AC: 41731 AN: 151746 Hom.: 5960 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.275 AC: 41793 AN: 151862 Hom.: 5978 Cov.: 32 AF XY: 0.280 AC XY: 20809 AN XY: 74214

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.251

Alfa AF: 0.247 Hom.: 5809

Bravo AF: 0.275

Asia WGS AF: 0.290 AC: 1004 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013209; hg19: chr8-24116304;