20-1811274-T-G

Variant summary

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

The ENST00000447206.1(ENSG00000286288):n.39-50A>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 0.568 in 151,924 control chromosomes in the GnomAD database, including 25,072 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 0.57 (25057 hom., cov: 30)
  • Exomes 𝑓: 0.62 (15 hom.)
• Consequence: ENST00000447206.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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
	ENST00000447206.1	n.39-50A>C		intron_variant, non_coding_transcript_variant		2
	ENST00000654380.1	n.81-600A>C		intron_variant, non_coding_transcript_variant
	ENST00000658107.1	n.92-600A>C		intron_variant, non_coding_transcript_variant
	ENST00000661517.1	n.198-600A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86119 AN: 151732 Hom.: 25038 Cov.: 30

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.601

GnomAD4 exome AF: 0.622 AC: 46 AN: 74 Hom.: 15 Cov.: 0 AF XY: 0.640 AC XY: 32 AN XY: 50

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.672

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.567 AC: 86172 AN: 151850 Hom.: 25057 Cov.: 30 AF XY: 0.566 AC XY: 41978 AN XY: 74206

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.602

Alfa AF: 0.612 Hom.: 34517

Bravo AF: 0.575

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200891; hg19: chr20-1791920;