20-53688088-C-T

Variant names:

• chr20-53688088-C-T
• rs6022662
• ENST00000716917.1:n.504-52316C>T

Variant summary

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

The ENST00000716917.1(ENSG00000293654):​n.504-52316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,066 control chromosomes in the GnomAD database, including 6,708 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 0.27 (6708 hom., cov: 33)
• Consequence: ENSG00000293654 ENST00000716917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 1 publications found

Genes affected

ENSG00000293654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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
ENSG00000293654	ENST00000716917.1	n.504-52316C>T		intron_variant	Intron 2 of 2
ENSG00000293654	ENST00000716918.1	n.340-52316C>T		intron_variant	Intron 1 of 1
ENSG00000235415	ENST00000716921.1	n.610-8073C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40799 AN: 151948 Hom.: 6678 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.269 AC: 40876 AN: 152066 Hom.: 6708 Cov.: 33 AF XY: 0.268 AC XY: 19931 AN XY: 74318

African (AFR) AF: 0.459 AC: 19030 AN: 41496

American (AMR) AF: 0.246 AC: 3747 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1150 AN: 5168

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4812

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10556

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12647 AN: 68006

Other (OTH) AF: 0.254 AC: 538 AN: 2114

Alfa AF: 0.103 Hom.: 155

Bravo AF: 0.285

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6022662; hg19: chr20-52304627;