rs2855039

chr11-5250441-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 0.246 in 152,048 control chromosomes in the GnomAD database, including 5,152 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 0.25 (5152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

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 (NFE) allele frequency at 95% confidence interval = 0.317 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: 0.246 AC: 37348 AN: 151930 Hom.: 5155 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.246 AC: 37352 AN: 152048 Hom.: 5152 Cov.: 32 AF XY: 0.241 AC XY: 17889 AN XY: 74324

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.253

Alfa AF: 0.299 Hom.: 13407

Bravo AF: 0.237

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.065
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2855039; hg19: chr11-5271671;