20-48554800-A-G

Variant names:

• chr20-48554800-A-G
• rs1883888
• ENST00000727174.1:n.342+8483T>C

Variant summary

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

The ENST00000727174.1(ENSG00000294979):​n.342+8483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,986 control chromosomes in the GnomAD database, including 35,886 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 0.68 (35886 hom., cov: 30)
• Consequence: ENSG00000294979 ENST00000727174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 6 publications found

Genes affected

ENSG00000294979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727174.1. 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
	ENSG00000294979	ENST00000727174.1		n.342+8483T>C		intron	N/A
	ENSG00000294979	ENST00000727175.1		n.339+8483T>C		intron	N/A
	ENSG00000294979	ENST00000727176.1		n.342+8483T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103923 AN: 151868 Hom.: 35832 Cov.: 30

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.685 AC: 104038 AN: 151986 Hom.: 35886 Cov.: 30 AF XY: 0.685 AC XY: 50872 AN XY: 74268

African (AFR) AF: 0.633 AC: 26227 AN: 41448

American (AMR) AF: 0.745 AC: 11382 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2416 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3221 AN: 5158

South Asian (SAS) AF: 0.545 AC: 2609 AN: 4790

European-Finnish (FIN) AF: 0.759 AC: 8023 AN: 10566

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47862 AN: 67952

Other (OTH) AF: 0.669 AC: 1414 AN: 2114

Alfa AF: 0.695 Hom.: 157543

Bravo AF: 0.686

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.44
PhyloP100		-0.91

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1883888;

hg19: chr20-47171338;