rs11246867

chr12-131893472-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903059 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903059	XR_007063538.1	n.416C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0736

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0793 Hom.: 1298

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11246867; hg19: chr12-132378017;