20-54182662-T-C

Position:

• chr20-54182662-T-C

Variant summary

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

The ENST00000655028.1(ENSG00000286587):​n.182T>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 0.58 in 152,048 control chromosomes in the GnomAD database, including 25,850 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 0.58 (25850 hom., cov: 31)
• Consequence: ENSG00000286587 ENST00000655028.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.274+28T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000655028.1	n.182T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88164 AN: 151930 Hom.: 25835 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.553

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.580 AC: 88214 AN: 152048 Hom.: 25850 Cov.: 31 AF XY: 0.579 AC XY: 43061 AN XY: 74312

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.550

Alfa AF: 0.591 Hom.: 8300

Bravo AF: 0.578

Asia WGS AF: 0.488 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6068821; hg19: chr20-52799201;