XR_007063538.1:n.416C>T

Variant names:

• chr12-131893472-G-A
• rs11246867
• XR_007063538.1:n.416C>T

Variant summary

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

The XR_007063538.1(LOC124903059):​n.416C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,156 control chromosomes in the GnomAD database, including 4,960 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 0.18 (4960 hom., cov: 32)
• Consequence: LOC124903059 XR_007063538.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 10 publications found

Genes affected

LOC124903059 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.180 AC: 27314 AN: 152038 Hom.: 4956 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0737

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.180 AC: 27346 AN: 152156 Hom.: 4960 Cov.: 32 AF XY: 0.177 AC XY: 13205 AN XY: 74412

African (AFR) AF: 0.466 AC: 19323 AN: 41466

American (AMR) AF: 0.0991 AC: 1515 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3472

East Asian (EAS) AF: 0.0736 AC: 382 AN: 5188

South Asian (SAS) AF: 0.117 AC: 565 AN: 4832

European-Finnish (FIN) AF: 0.0695 AC: 737 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0581 AC: 3948 AN: 67998

Other (OTH) AF: 0.152 AC: 320 AN: 2110

Alfa AF: 0.0927 Hom.: 2479

Bravo AF: 0.195

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11246867; hg19: chr12-132378017;