20-23053637-T-G

Variant names:

• chr20-23053637-T-G
• rs6048519
• ENST00000739778.1:n.302+3157T>G

Variant summary

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

The ENST00000739778.1(ENSG00000296463):​n.302+3157T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,016 control chromosomes in the GnomAD database, including 21,523 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 0.51 (21523 hom., cov: 32)
• Consequence: ENSG00000296463 ENST00000739778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 10 publications found

Genes affected

ENSG00000296463 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739778.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296463	ENST00000739778.1		n.302+3157T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77076 AN: 151898 Hom.: 21478 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.508 AC: 77166 AN: 152016 Hom.: 21523 Cov.: 32 AF XY: 0.511 AC XY: 37999 AN XY: 74322

African (AFR) AF: 0.748 AC: 30981 AN: 41416

American (AMR) AF: 0.430 AC: 6567 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2771 AN: 5172

South Asian (SAS) AF: 0.410 AC: 1975 AN: 4814

European-Finnish (FIN) AF: 0.550 AC: 5823 AN: 10584

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26343 AN: 67978

Other (OTH) AF: 0.456 AC: 964 AN: 2112

Alfa AF: 0.422 Hom.: 45510

Bravo AF: 0.510

Asia WGS AF: 0.452 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6048519; hg19: chr20-23034274;