chr12-30129954-A-G

Position:

• chr12-30129954-A-G

Variant summary

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

The ENST00000653361.1(ENSG00000286566):​n.279-373A>G 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 0.407 in 152,054 control chromosomes in the GnomAD database, including 13,647 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 0.41 (13647 hom., cov: 33)
• Consequence: ENST00000653361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653361.1	n.279-373A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61806 AN: 151936 Hom.: 13631 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.407 AC: 61861 AN: 152054 Hom.: 13647 Cov.: 33 AF XY: 0.405 AC XY: 30141 AN XY: 74336

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.406

Alfa AF: 0.474 Hom.: 17222

Bravo AF: 0.395

Asia WGS AF: 0.391 AC: 1357 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	0.48
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1485405; hg19: chr12-30282887;