rs12808148

Variant names:

• chr11-102862432-T-C
• rs12808148
• XR_007062868.1:n.1992-2766T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062868.1(LOC124902741):​n.1992-2766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,246 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 26 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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: 0.120 AC: 18275 AN: 152128 Hom.: 1289 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.120 AC: 18263 AN: 152246 Hom.: 1288 Cov.: 32 AF XY: 0.120 AC XY: 8924 AN XY: 74436

African (AFR) AF: 0.0585 AC: 2432 AN: 41560

American (AMR) AF: 0.109 AC: 1671 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3472

East Asian (EAS) AF: 0.0670 AC: 347 AN: 5178

South Asian (SAS) AF: 0.0987 AC: 476 AN: 4822

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10602

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10328 AN: 67998

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.139 Hom.: 1479

Bravo AF: 0.111

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.36
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12808148; hg19: chr11-102733163;