20-53652456-T-G

Variant names:

• chr20-53652456-T-G
• rs2041278
• ENST00000716917.1:n.503+34458T>G

Variant summary

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

The ENST00000716917.1(ENSG00000293654):​n.503+34458T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,020 control chromosomes in the GnomAD database, including 26,242 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 0.57 (26242 hom., cov: 33)
• Consequence: ENSG00000293654 ENST00000716917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 12 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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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.503+34458T>G		intron_variant	Intron 2 of 2
ENSG00000293654	ENST00000716918.1	n.339+43945T>G		intron_variant	Intron 1 of 1
ENSG00000235415	ENST00000716920.1	n.540-20368T>G		intron_variant	Intron 2 of 3
ENSG00000235415	ENST00000716921.1	n.340-20368T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85938 AN: 151902 Hom.: 26246 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.565 AC: 85946 AN: 152020 Hom.: 26242 Cov.: 33 AF XY: 0.568 AC XY: 42215 AN XY: 74324

African (AFR) AF: 0.322 AC: 13356 AN: 41432

American (AMR) AF: 0.562 AC: 8566 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2275 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3667 AN: 5178

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4818

European-Finnish (FIN) AF: 0.731 AC: 7730 AN: 10576

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45888 AN: 67976

Other (OTH) AF: 0.579 AC: 1224 AN: 2114

Alfa AF: 0.629 Hom.: 99337

Bravo AF: 0.543

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	17
DANN	Benign	0.67
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2041278; hg19: chr20-52268995;