rs2077224

Positions:

• chr11-62429955-C-A

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 0.336 in 152,106 control chromosomes in the GnomAD database, including 8,857 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 0.34 (8857 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.336 AC: 51006 AN: 151988 Hom.: 8850 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.336 AC: 51040 AN: 152106 Hom.: 8857 Cov.: 33 AF XY: 0.330 AC XY: 24564 AN XY: 74350

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.331

Alfa AF: 0.360 Hom.: 4667

Bravo AF: 0.334

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077224; hg19: chr11-62197427;