XR_007063492.1:n.5382C>T

Variant names:

• chr12-121087614-G-A
• rs12819523
• XR_007063492.1:n.5382C>T

Variant summary

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

The XR_007063492.1(LOC105378258):​n.5382C>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 0.0529 in 152,302 control chromosomes in the GnomAD database, including 268 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 0.053 (268 hom., cov: 32)
• Consequence: LOC105378258 XR_007063492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 4 publications found

Genes affected

LOC105378258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378258	XR_007063492.1	n.5382C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105378258	XR_945451.4	n.5382C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308947	ENST00000837477.1	n.540+199G>A		intron_variant	Intron 2 of 2
ENSG00000308932	ENST00000837362.1	n.*243C>T		downstream_gene_variant
ENSG00000308932	ENST00000837363.1	n.*243C>T		downstream_gene_variant
ENSG00000308932	ENST00000837364.1	n.*243C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8052 AN: 152184 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0529 AC: 8063 AN: 152302 Hom.: 268 Cov.: 32 AF XY: 0.0534 AC XY: 3973 AN XY: 74470

African (AFR) AF: 0.0242 AC: 1007 AN: 41570

American (AMR) AF: 0.0677 AC: 1035 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 139 AN: 3472

East Asian (EAS) AF: 0.0545 AC: 282 AN: 5176

South Asian (SAS) AF: 0.0952 AC: 460 AN: 4830

European-Finnish (FIN) AF: 0.0538 AC: 571 AN: 10610

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4342 AN: 68026

Other (OTH) AF: 0.0595 AC: 126 AN: 2116

Alfa AF: 0.0515 Hom.: 33

Bravo AF: 0.0514

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.54
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs12819523; hg19: chr12-121525417;