20-23139129-C-T

Variant names:

• chr20-23139129-C-T
• rs6083017
• ENST00000751532.1:n.434C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751532.1(ENSG00000297882):​n.434C>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 0.611 in 152,114 control chromosomes in the GnomAD database, including 28,717 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 (28717 hom., cov: 33)
• Consequence: ENSG00000297882 ENST00000751532.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 3 publications found

Genes affected

ENSG00000297882 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751532.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297882	ENST00000751532.1		n.434C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92847 AN: 151996 Hom.: 28692 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.611 AC: 92908 AN: 152114 Hom.: 28717 Cov.: 33 AF XY: 0.605 AC XY: 44967 AN XY: 74360

African (AFR) AF: 0.549 AC: 22758 AN: 41478

American (AMR) AF: 0.674 AC: 10310 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2701 AN: 5182

South Asian (SAS) AF: 0.596 AC: 2873 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5480 AN: 10572

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44157 AN: 67988

Other (OTH) AF: 0.657 AC: 1387 AN: 2110

Alfa AF: 0.647 Hom.: 53183

Bravo AF: 0.622

Asia WGS AF: 0.593 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.46
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs6083017; hg19: chr20-23119766;