11-630124-A-G

Position:

• chr11-630124-A-G

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 0.357 in 151,600 control chromosomes in the GnomAD database, including 11,016 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 0.36 (11016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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 (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.357 AC: 54071 AN: 151482 Hom.: 10997 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0305

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.357 AC: 54131 AN: 151600 Hom.: 11016 Cov.: 31 AF XY: 0.347 AC XY: 25712 AN XY: 74046

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.349

Alfa AF: 0.315 Hom.: 4651

Bravo AF: 0.375

Asia WGS AF: 0.144 AC: 502 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	0.60
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11246221; hg19: chr11-630124;