20-2477142-G-T

Variant names:

• chr20-2477142-G-T
• rs1109009
• ENST00000461548.1:n.305-9384C>A

Variant summary

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

The ENST00000461548.1(ENSG00000256566):​n.305-9384C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,978 control chromosomes in the GnomAD database, including 33,174 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 0.64 (33174 hom., cov: 32)
• Consequence: ENSG00000256566 ENST00000461548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 14 publications found

Genes affected

ENSG00000256566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 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
ENSG00000256566	ENST00000461548.1	n.305-9384C>A		intron_variant	Intron 5 of 6	5		ENSP00000456213.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97786 AN: 151860 Hom.: 33161 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.644 AC: 97831 AN: 151978 Hom.: 33174 Cov.: 32 AF XY: 0.642 AC XY: 47688 AN XY: 74284

African (AFR) AF: 0.415 AC: 17191 AN: 41422

American (AMR) AF: 0.718 AC: 10975 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2497 AN: 3472

East Asian (EAS) AF: 0.717 AC: 3702 AN: 5162

South Asian (SAS) AF: 0.611 AC: 2938 AN: 4812

European-Finnish (FIN) AF: 0.657 AC: 6927 AN: 10540

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51294 AN: 67980

Other (OTH) AF: 0.672 AC: 1417 AN: 2110

Alfa AF: 0.713 Hom.: 122922

Bravo AF: 0.639

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.3
DANN	Benign	0.62
PhyloP100		0.053

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1109009; hg19: chr20-2457788;