chr20-48522907-A-G

Variant names:

• chr20-48522907-A-G
• rs12481537
• ENST00000727053.1:n.325+822A>G

Variant summary

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

The ENST00000727053.1(ENSG00000294963):​n.325+822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,096 control chromosomes in the GnomAD database, including 24,609 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 0.56 (24609 hom., cov: 33)
• Consequence: ENSG00000294963 ENST00000727053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 1 publications found

Genes affected

ENSG00000294963 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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
ENSG00000294963	ENST00000727053.1	n.325+822A>G		intron_variant	Intron 3 of 4
ENSG00000294963	ENST00000727054.1	n.235+822A>G		intron_variant	Intron 2 of 3
ENSG00000294963	ENST00000727055.1	n.307+822A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84415 AN: 151978 Hom.: 24565 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.556 AC: 84508 AN: 152096 Hom.: 24609 Cov.: 33 AF XY: 0.555 AC XY: 41294 AN XY: 74354

African (AFR) AF: 0.724 AC: 30029 AN: 41486

American (AMR) AF: 0.472 AC: 7204 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3860 AN: 5168

South Asian (SAS) AF: 0.622 AC: 3002 AN: 4824

European-Finnish (FIN) AF: 0.451 AC: 4773 AN: 10572

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32664 AN: 67988

Other (OTH) AF: 0.510 AC: 1074 AN: 2104

Alfa AF: 0.518 Hom.: 4698

Bravo AF: 0.560

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.50
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs12481537; hg19: chr20-47139445;