20-54180142-C-G

Position:

• chr20-54180142-C-G

Variant summary

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

The ENST00000655028.1(ENSG00000286587):​n.75+1654C>G 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 0.104 in 152,202 control chromosomes in the GnomAD database, including 1,129 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 0.10 (1129 hom., cov: 33)
• Consequence: ENST00000655028.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.195+1654C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655028.1	n.75+1654C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15832 AN: 152084 Hom.: 1128 Cov.: 33

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.104 AC: 15838 AN: 152202 Hom.: 1129 Cov.: 33 AF XY: 0.103 AC XY: 7697 AN XY: 74416

Gnomad4 AFR AF: 0.0327

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0582 Hom.: 60

Bravo AF: 0.101

Asia WGS AF: 0.163 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2426498; hg19: chr20-52796681;