rs1326021

Positions:

• chr20-56269090-C-T

Variant summary

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

The ENST00000458731.1(ENSG00000235594):​n.954C>T 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 0.647 in 152,096 control chromosomes in the GnomAD database, including 33,134 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 0.65 (33133 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000235594 ENST00000458731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

ENSG00000235594 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56269090C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000235594	ENST00000458731.1	n.954C>T		non_coding_transcript_exon_variant	2/2	6

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98338 AN: 151968 Hom.: 33133 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.671

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 AFR exome AF: 0.250

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.647 AC: 98366 AN: 152086 Hom.: 33133 Cov.: 32 AF XY: 0.651 AC XY: 48400 AN XY: 74342

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.669

Alfa AF: 0.695 Hom.: 17151

Bravo AF: 0.642

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1326021; hg19: chr20-54844146;