rs12910772

chr15-36882201-C-Achr15-36882201-C-Gchr15-36882201-C-T

Variant summary

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

The NR_024264.1(LOC145845):n.316+129G>T 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 0.154 in 152,108 control chromosomes in the GnomAD database, including 1,857 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 0.15 (1856 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: LOC145845 NR_024264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC145845	NR_024264.1	n.316+129G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690156.1	n.117-533G>T		intron_variant, non_coding_transcript_variant
	ENST00000558089.1	n.316+129G>T		intron_variant, non_coding_transcript_variant		4
	ENST00000561259.1	n.100-533G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000693618.1	n.113-533G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23355 AN: 151974 Hom.: 1851 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.167 AC: 3 AN: 18 Hom.: 1 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.214

GnomAD4 genome AF: 0.154 AC: 23388 AN: 152090 Hom.: 1856 Cov.: 32 AF XY: 0.154 AC XY: 11468 AN XY: 74366

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.166

Alfa AF: 0.147 Hom.: 2394

Bravo AF: 0.153

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.072
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12910772; hg19: chr15-37174402;