chr20-2477241-G-A

Variant names:

• chr20-2477241-G-A
• rs1109010
• ENST00000461548.1:n.305-9483C>T

Variant summary

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

The ENST00000461548.1(ENSG00000256566):​n.305-9483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,126 control chromosomes in the GnomAD database, including 1,632 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 0.14 (1632 hom., cov: 32)
• Consequence: ENSG00000256566 ENST00000461548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 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.305-9483C>T		intron_variant	Intron 5 of 6	5		ENSP00000456213.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21270 AN: 152008 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.140 AC: 21271 AN: 152126 Hom.: 1632 Cov.: 32 AF XY: 0.143 AC XY: 10635 AN XY: 74340

African (AFR) AF: 0.165 AC: 6854 AN: 41506

American (AMR) AF: 0.154 AC: 2356 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3464

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5168

South Asian (SAS) AF: 0.189 AC: 908 AN: 4816

European-Finnish (FIN) AF: 0.170 AC: 1794 AN: 10556

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7256 AN: 68000

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.116 Hom.: 1876

Bravo AF: 0.141

Asia WGS AF: 0.239 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		0.16

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: rs1109010; hg19: chr20-2457887;