rs2282477

Positions:

• chr11-62889032-T-C

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 0.196 in 152,148 control chromosomes in the GnomAD database, including 3,009 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 0.20 (3009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 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: 0.196 AC: 29858 AN: 152026 Hom.: 3009 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.196 AC: 29877 AN: 152148 Hom.: 3009 Cov.: 32 AF XY: 0.198 AC XY: 14746 AN XY: 74390

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.199

Alfa AF: 0.206 Hom.: 3125

Bravo AF: 0.198

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282477; hg19: chr11-62656504;