rs871249

Variant names:

• chr11-48262925-G-A
• rs871249

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 0.279 in 152,018 control chromosomes in the GnomAD database, including 6,318 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 (6318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 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: 0.279 AC: 42369 AN: 151900 Hom.: 6301 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.279 AC: 42431 AN: 152018 Hom.: 6318 Cov.: 32 AF XY: 0.281 AC XY: 20892 AN XY: 74310

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.297

Alfa AF: 0.260 Hom.: 10833

Bravo AF: 0.283

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs871249; hg19: chr11-48284477;