chr20-56269090-C-T

Variant names:

• chr20-56269090-C-T
• rs1326021
• ENST00000458731.1:n.954C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000235594 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235594	ENST00000458731.1	n.954C>T		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.451 AC: 18677 AN: 41436

American (AMR) AF: 0.764 AC: 11696 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2273 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4480 AN: 5180

South Asian (SAS) AF: 0.771 AC: 3713 AN: 4814

European-Finnish (FIN) AF: 0.707 AC: 7475 AN: 10572

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47653 AN: 67990

Other (OTH) AF: 0.669 AC: 1416 AN: 2116

Alfa AF: 0.694 Hom.: 27298

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1326021; hg19: chr20-54844146;