11-2284938-C-T

Position:

• chr11-2284938-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 0.41 in 151,944 control chromosomes in the GnomAD database, including 13,181 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 0.41 (13181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62246 AN: 151826 Hom.: 13166 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.410 AC: 62292 AN: 151944 Hom.: 13181 Cov.: 32 AF XY: 0.408 AC XY: 30288 AN XY: 74238

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.389

Alfa AF: 0.381 Hom.: 16759

Bravo AF: 0.408

Asia WGS AF: 0.510 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7104786; hg19: chr11-2306168;