11-124844984-G-A

Position:

• chr11-124844984-G-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 0.254 in 152,112 control chromosomes in the GnomAD database, including 5,509 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 (5509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.254 AC: 38553 AN: 151994 Hom.: 5487 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.254 AC: 38632 AN: 152112 Hom.: 5509 Cov.: 32 AF XY: 0.258 AC XY: 19208 AN XY: 74344

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.221

Alfa AF: 0.228 Hom.: 731

Bravo AF: 0.267

Asia WGS AF: 0.274 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.012
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733601; hg19: chr11-124714880;