11-100578431-T-C

Variant names:

• chr11-100578431-T-C
• rs11224294

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 0.102 in 152,240 control chromosomes in the GnomAD database, including 994 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 0.10 (994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15490 AN: 152120 Hom.: 993 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.102 AC: 15493 AN: 152240 Hom.: 994 Cov.: 32 AF XY: 0.108 AC XY: 8003 AN XY: 74430

African (AFR) AF: 0.0608 AC: 2528 AN: 41560

American (AMR) AF: 0.114 AC: 1750 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5172

South Asian (SAS) AF: 0.121 AC: 580 AN: 4812

European-Finnish (FIN) AF: 0.183 AC: 1945 AN: 10606

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0928 AC: 6311 AN: 68008

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.0933 Hom.: 434

Bravo AF: 0.0947

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.65
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs11224294; hg19: chr11-100449162;