20-54174437-G-C

Variant names:

• chr20-54174437-G-C
• rs2585427
• ENST00000655028.2:n.393-316G>C

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.393-316G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 150,668 control chromosomes in the GnomAD database, including 16,510 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 0.45 (16510 hom., cov: 27)
• Consequence: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 8 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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
ENSG00000286587	ENST00000655028.2	n.393-316G>C		intron_variant	Intron 2 of 4
ENSG00000286587	ENST00000792273.1	n.288+5866G>C		intron_variant	Intron 3 of 3
ENSG00000286587	ENST00000792274.1	n.279-3955G>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68095 AN: 150560 Hom.: 16467 Cov.: 27

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.453 AC: 68186 AN: 150668 Hom.: 16510 Cov.: 27 AF XY: 0.449 AC XY: 33042 AN XY: 73576

African (AFR) AF: 0.644 AC: 26337 AN: 40890

American (AMR) AF: 0.354 AC: 5394 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3466

East Asian (EAS) AF: 0.368 AC: 1850 AN: 5034

South Asian (SAS) AF: 0.405 AC: 1931 AN: 4770

European-Finnish (FIN) AF: 0.349 AC: 3622 AN: 10374

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25764 AN: 67592

Other (OTH) AF: 0.457 AC: 961 AN: 2104

Alfa AF: 0.233 Hom.: 450

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.34
PhyloP100		-1.2
PromoterAI		0.0060	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2585427; hg19: chr20-52790976;