rs1449460

Positions:

• chr12-78442167-A-G

Variant summary

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

The ENST00000547569.1(ENSG00000257879):​n.786T>C 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 0.0619 in 152,114 control chromosomes in the GnomAD database, including 446 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 0.062 (446 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENST00000547569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

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 (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000547569.1	n.786T>C		non_coding_transcript_exon_variant	1/3	4
	ENST00000552230.5	n.163-35226A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9418 AN: 151990 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0689

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0619 AC: 9415 AN: 152108 Hom.: 446 Cov.: 32 AF XY: 0.0645 AC XY: 4797 AN XY: 74368

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.0540

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0724 Hom.: 623

Bravo AF: 0.0584

Asia WGS AF: 0.159 AC: 552 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	1.7
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: rs1449460; hg19: chr12-78835947;