rs11246867

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903059	XR_007063538.1	n.416C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;