12-114949991-T-C

Position:

• chr12-114949991-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063587.1(LOC124903080):​n.1832T>C 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 0.346 in 152,020 control chromosomes in the GnomAD database, including 9,806 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 0.35 (9806 hom., cov: 32)
• Consequence: LOC124903080 XR_007063587.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

Genes affected

LOC124903080 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903080	XR_007063587.1	n.1832T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52599 AN: 151902 Hom.: 9788 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.346 AC: 52643 AN: 152020 Hom.: 9806 Cov.: 32 AF XY: 0.356 AC XY: 26449 AN XY: 74280

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.371

Alfa AF: 0.316 Hom.: 13860

Bravo AF: 0.352

Asia WGS AF: 0.611 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10850411; hg19: chr12-115387796;