chr20-57717823-C-T

Variant names:

• chr20-57717823-C-T
• rs8118851
• ENST00000723794.1:n.633C>T

Variant summary

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

The ENST00000723794.1(ENSG00000294467):​n.633C>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 0.157 in 152,172 control chromosomes in the GnomAD database, including 1,990 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 0.16 (1990 hom., cov: 33)
• Consequence: ENSG00000294467 ENST00000723794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 2 publications found

Genes affected

ENSG00000294467 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294467	ENST00000723794.1	n.633C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23960 AN: 152054 Hom.: 1987 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.157 AC: 23967 AN: 152172 Hom.: 1990 Cov.: 33 AF XY: 0.156 AC XY: 11596 AN XY: 74382

African (AFR) AF: 0.189 AC: 7862 AN: 41512

American (AMR) AF: 0.105 AC: 1613 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5174

South Asian (SAS) AF: 0.187 AC: 904 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1423 AN: 10588

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10968 AN: 68000

Other (OTH) AF: 0.150 AC: 317 AN: 2112

Alfa AF: 0.156 Hom.: 2960

Bravo AF: 0.153

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.46
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs8118851; hg19: chr20-56292879;