20-54182040-G-T

Position:

• chr20-54182040-G-T

Variant summary

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

The ENST00000655028.1(ENSG00000286587):​n.76-516G>T 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 0.0821 in 152,282 control chromosomes in the GnomAD database, including 637 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 0.082 (637 hom., cov: 33)
• Consequence: ENST00000655028.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.196-516G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655028.1	n.76-516G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12488 AN: 152164 Hom.: 636 Cov.: 33

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.0821 AC: 12496 AN: 152282 Hom.: 637 Cov.: 33 AF XY: 0.0831 AC XY: 6186 AN XY: 74448

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0689

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.0806 Hom.: 608

Bravo AF: 0.0842

Asia WGS AF: 0.185 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585424; hg19: chr20-52798579;