20-11446082-A-G

Variant names:

• chr20-11446082-A-G
• rs10485749
• ENST00000784484.1:n.452+10187T>C

Variant summary

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

The ENST00000784484.1(ENSG00000282478):​n.452+10187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,094 control chromosomes in the GnomAD database, including 31,142 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 0.63 (31142 hom., cov: 32)
• Consequence: ENSG00000282478 ENST00000784484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 5 publications found

Genes affected

ENSG00000282478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784484.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282478	ENST00000784484.1		n.452+10187T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95586 AN: 151976 Hom.: 31132 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.629 AC: 95632 AN: 152094 Hom.: 31142 Cov.: 32 AF XY: 0.628 AC XY: 46716 AN XY: 74346

African (AFR) AF: 0.439 AC: 18225 AN: 41468

American (AMR) AF: 0.687 AC: 10491 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3421 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3812 AN: 4828

European-Finnish (FIN) AF: 0.619 AC: 6549 AN: 10576

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48274 AN: 68002

Other (OTH) AF: 0.666 AC: 1406 AN: 2110

Alfa AF: 0.693 Hom.: 20355

Bravo AF: 0.628

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10485749; hg19: chr20-11426730;