ENST00000803561.1:n.520-7507C>G

Variant names:

• chr20-45548848-C-G
• rs6124715
• ENST00000803561.1:n.520-7507C>G

Variant summary

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

The ENST00000803561.1(ENSG00000237464):​n.520-7507C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,784 control chromosomes in the GnomAD database, including 36,656 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 0.69 (36656 hom., cov: 30)
• Consequence: ENSG00000237464 ENST00000803561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 7 publications found

Genes affected

ENSG00000237464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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
ENSG00000237464	ENST00000803561.1	n.520-7507C>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105167 AN: 151666 Hom.: 36604 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.694 AC: 105283 AN: 151784 Hom.: 36656 Cov.: 30 AF XY: 0.691 AC XY: 51264 AN XY: 74176

African (AFR) AF: 0.725 AC: 29981 AN: 41370

American (AMR) AF: 0.723 AC: 11027 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3296 AN: 5146

South Asian (SAS) AF: 0.601 AC: 2885 AN: 4800

European-Finnish (FIN) AF: 0.692 AC: 7279 AN: 10516

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46537 AN: 67914

Other (OTH) AF: 0.686 AC: 1445 AN: 2106

Alfa AF: 0.686 Hom.: 4247

Bravo AF: 0.699

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.54
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6124715; hg19: chr20-44177487;