rs2008849

Variant names:

• chr11-129528916-C-T
• rs2008849

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 152,138 control chromosomes in the GnomAD database, including 6,077 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 (6077 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.275 AC: 41845 AN: 152020 Hom.: 6070 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.00461

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.275 AC: 41874 AN: 152138 Hom.: 6077 Cov.: 33 AF XY: 0.270 AC XY: 20045 AN XY: 74368

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.290

Alfa AF: 0.287 Hom.: 13201

Bravo AF: 0.275

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2008849; hg19: chr11-129398811;