rs12413088

chr10-121293214-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007062321.1(LOC105378523):n.515+20002G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,080 control chromosomes in the GnomAD database, including 2,995 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 (2995 hom., cov: 32)
• Consequence: LOC105378523 XR_007062321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

Genes affected

LOC105378523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378523	XR_007062321.1	n.515+20002G>A		intron_variant, non_coding_transcript_variant
LOC105378523	XR_007062320.1	n.516-1523G>A		intron_variant, non_coding_transcript_variant
LOC105378523	XR_946380.3	n.204-1523G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27052 AN: 151962 Hom.: 2997 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.178 AC: 27051 AN: 152080 Hom.: 2995 Cov.: 32 AF XY: 0.179 AC XY: 13329 AN XY: 74346

Gnomad4 AFR AF: 0.0512

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.205

Alfa AF: 0.216 Hom.: 2269

Bravo AF: 0.165

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	16
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12413088; hg19: chr10-123052728;