1-143544453-T-C

Variant summary

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

The ENST00000449715.1(ENSG00000203825):n.513+79T>C 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 0.772 in 655,426 control chromosomes in the GnomAD database, including 204,779 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 0.78 (46259 hom., cov: 28)
  • Exomes 𝑓: 0.77 (158520 hom.)
• Consequence: ENST00000449715.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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
	ENST00000449715.1	n.513+79T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.775 AC: 113457 AN: 146344 Hom.: 46218 Cov.: 28

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.770 AC: 392131 AN: 508964 Hom.: 158520 AF XY: 0.762 AC XY: 208853 AN XY: 274248

Gnomad4 AFR exome AF: 0.765

Gnomad4 AMR exome AF: 0.763

Gnomad4 ASJ exome AF: 0.781

Gnomad4 EAS exome AF: 0.857

Gnomad4 SAS exome AF: 0.627

Gnomad4 FIN exome AF: 0.826

Gnomad4 NFE exome AF: 0.779

Gnomad4 OTH exome AF: 0.775

GnomAD4 genome AF: 0.775 AC: 113550 AN: 146462 Hom.: 46259 Cov.: 28 AF XY: 0.773 AC XY: 55133 AN XY: 71364

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.761

Alfa AF: 0.741 Hom.: 10669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11579261; hg19: chr1-149039120;