11-23461398-C-T

Variant names:

• chr11-23461398-C-T
• rs12146457

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 0.138 in 151,326 control chromosomes in the GnomAD database, including 1,726 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 0.14 (1726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20831 AN: 151216 Hom.: 1723 Cov.: 31

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.138 AC: 20844 AN: 151326 Hom.: 1726 Cov.: 31 AF XY: 0.137 AC XY: 10123 AN XY: 73908

African (AFR) AF: 0.0477 AC: 1971 AN: 41328

American (AMR) AF: 0.174 AC: 2623 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3458

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5132

South Asian (SAS) AF: 0.111 AC: 534 AN: 4818

European-Finnish (FIN) AF: 0.190 AC: 1979 AN: 10432

Middle Eastern (MID) AF: 0.253 AC: 73 AN: 288

European-Non Finnish (NFE) AF: 0.185 AC: 12550 AN: 67758

Other (OTH) AF: 0.163 AC: 340 AN: 2092

Alfa AF: 0.174 Hom.: 3373

Bravo AF: 0.130

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12146457; hg19: chr11-23482944;