rs10466868

Positions:

• chr12-131455375-G-T

Variant summary

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

The NR_187798.1(LOC101929974):​n.3486C>A 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 0.0741 in 152,576 control chromosomes in the GnomAD database, including 576 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 0.074 (575 hom., cov: 33)
  • Exomes 𝑓: 0.090 (1 hom.)
• Consequence: LOC101929974 NR_187798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551

Genes affected

LOC101929974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929974	NR_187798.1	n.3486C>A		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000275232	ENST00000618927.1	n.39+23C>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11285 AN: 152058 Hom.: 575 Cov.: 33

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0791

GnomAD4 exome AF: 0.0900 AC: 36 AN: 400 Hom.: 1 Cov.: 0 AF XY: 0.100 AC XY: 30 AN XY: 300

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.0920

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0741 AC: 11275 AN: 152176 Hom.: 575 Cov.: 33 AF XY: 0.0723 AC XY: 5378 AN XY: 74396

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0778

Alfa AF: 0.101 Hom.: 1832

Bravo AF: 0.0723

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	4.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10466868; hg19: chr12-131939920;