11-630124-A-G

Variant names:

• chr11-630124-A-G
• rs11246221

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.552 AC: 22805 AN: 41322

American (AMR) AF: 0.324 AC: 4921 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3466

East Asian (EAS) AF: 0.0305 AC: 157 AN: 5142

South Asian (SAS) AF: 0.158 AC: 756 AN: 4798

European-Finnish (FIN) AF: 0.231 AC: 2424 AN: 10516

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20714 AN: 67850

Other (OTH) AF: 0.349 AC: 733 AN: 2098

Alfa AF: 0.318 Hom.: 6099

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11246221; hg19: chr11-630124;