rs871249

Variant names:

• chr11-48262925-G-A
• rs871249

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.333 AC: 13794 AN: 41456

American (AMR) AF: 0.252 AC: 3854 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3464

East Asian (EAS) AF: 0.423 AC: 2178 AN: 5154

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4814

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16490 AN: 67966

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.263 Hom.: 17301

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
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs871249; hg19: chr11-48284477;