12-5022387-T-G

Position:

• chr12-5022387-T-G

Variant summary

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

The ENST00000540533.2(ENSG00000256654):​n.1285T>G 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 0.394 in 152,124 control chromosomes in the GnomAD database, including 12,672 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 0.39 (12672 hom., cov: 33)
  • Exomes 𝑓: 0.44 (0 hom.)
• Consequence: ENSG00000256654 ENST00000540533.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

Genes affected

ENSG00000256654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507560	NR_187672.1	n.4121-104T>G		intron_variant
LOC100507560	NR_187673.1	n.4047-104T>G		intron_variant
LOC100507560	NR_187674.1	n.4121-104T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256654	ENST00000540533.2	n.1285T>G		non_coding_transcript_exon_variant	2/4	5
ENSG00000256654	ENST00000639114.2	n.1001T>G		non_coding_transcript_exon_variant	1/3	5
ENSG00000256654	ENST00000638455.1	n.610-104T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59919 AN: 151990 Hom.: 12660 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.388

GnomAD4 exome AF: 0.438 AC: 7 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.429

GnomAD4 genome AF: 0.394 AC: 59961 AN: 152108 Hom.: 12672 Cov.: 33 AF XY: 0.400 AC XY: 29761 AN XY: 74364

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.391

Alfa AF: 0.288 Hom.: 990

Bravo AF: 0.397

Asia WGS AF: 0.702 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16932667; hg19: chr12-5131553;