rs2508746

Variant names:

• chr11-76559906-C-T
• rs2508746

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 0.425 in 151,918 control chromosomes in the GnomAD database, including 14,279 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 0.43 (14279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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: 0.425 AC: 64538 AN: 151800 Hom.: 14276 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 64572 AN: 151918 Hom.: 14279 Cov.: 31 AF XY: 0.419 AC XY: 31108 AN XY: 74242

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.430

Alfa AF: 0.467 Hom.: 22931

Bravo AF: 0.418

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2508746; hg19: chr11-76270950;