20-39388459-G-C

Variant names:

• chr20-39388459-G-C
• rs2179443
• ENST00000772859.1:n.459-13115G>C

Variant summary

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

The ENST00000772859.1(ENSG00000300599):​n.459-13115G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,004 control chromosomes in the GnomAD database, including 17,730 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 0.47 (17730 hom., cov: 32)
• Consequence: ENSG00000300599 ENST00000772859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

ENSG00000300599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772859.1. 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
	ENSG00000300599	ENST00000772859.1		n.459-13115G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71326 AN: 151884 Hom.: 17716 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.470 AC: 71368 AN: 152004 Hom.: 17730 Cov.: 32 AF XY: 0.479 AC XY: 35566 AN XY: 74302

African (AFR) AF: 0.340 AC: 14079 AN: 41422

American (AMR) AF: 0.596 AC: 9104 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2120 AN: 3468

East Asian (EAS) AF: 0.758 AC: 3921 AN: 5170

South Asian (SAS) AF: 0.710 AC: 3428 AN: 4826

European-Finnish (FIN) AF: 0.492 AC: 5199 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31958 AN: 67966

Other (OTH) AF: 0.465 AC: 982 AN: 2114

Alfa AF: 0.466 Hom.: 2085

Bravo AF: 0.468

Asia WGS AF: 0.756 AC: 2624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.55
PhyloP100		0.0010

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: rs2179443;

hg19: chr20-38017102;