20-54189737-T-C

Position:

• chr20-54189737-T-C

Variant summary

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

The XR_936882.4(LOC105372675):​n.457T>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 0.613 in 152,036 control chromosomes in the GnomAD database, including 28,753 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 0.61 (28753 hom., cov: 32)
• Consequence: LOC105372675 XR_936882.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

LOC105372675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.457T>C		non_coding_transcript_exon_variant	4/4
		n.54189737T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93167 AN: 151918 Hom.: 28738 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.613 AC: 93218 AN: 152036 Hom.: 28753 Cov.: 32 AF XY: 0.615 AC XY: 45707 AN XY: 74332

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.584

Alfa AF: 0.608 Hom.: 11423

Bravo AF: 0.611

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.0
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6023009; hg19: chr20-52806276;