20-51098572-C-T

Position:

• chr20-51098572-C-T

Variant summary

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

The ENST00000624745.1(ENSG00000279835):​n.435C>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 0.117 in 152,274 control chromosomes in the GnomAD database, including 1,094 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 0.12 (1094 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: ENSG00000279835 ENST00000624745.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

Genes affected

ENSG00000279835 (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 (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51098572C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279835	ENST00000624745.1	n.435C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17748 AN: 152128 Hom.: 1095 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.115 AC: 3 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.136

GnomAD4 genome AF: 0.117 AC: 17761 AN: 152248 Hom.: 1094 Cov.: 32 AF XY: 0.112 AC XY: 8368 AN XY: 74438

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.128

Alfa AF: 0.116 Hom.: 1179

Bravo AF: 0.121

Asia WGS AF: 0.0560 AC: 195 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	0.25
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16995730; hg19: chr20-49715109;