rs12300899

Positions:

• chr12-125062029-C-T

Variant summary

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

The XR_001749365.2(LOC105370052):​n.303-720G>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 0.139 in 137,538 control chromosomes in the GnomAD database, including 1,542 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 0.14 (1542 hom., cov: 30)
• Consequence: LOC105370052 XR_001749365.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

Genes affected

LOC105370052 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370052	XR_001749365.2	n.303-720G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 19155 AN: 137494 Hom.: 1538 Cov.: 30

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 19170 AN: 137538 Hom.: 1542 Cov.: 30 AF XY: 0.148 AC XY: 9835 AN XY: 66358

Gnomad4 AFR AF: 0.0728

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0180 Hom.: 14

Bravo AF: 0.125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12300899; hg19: chr12-125546575;