20-4638511-A-G

Variant names:

• chr20-4638511-A-G
• rs4813709
• ENST00000652447.1:n.88-8290T>C

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.88-8290T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,108 control chromosomes in the GnomAD database, including 22,454 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 0.53 (22454 hom., cov: 33)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 1 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.618 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
ENSG00000293214	ENST00000652447.1	n.88-8290T>C		intron_variant	Intron 1 of 1
ENSG00000293214	ENST00000773443.1	n.132-8290T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80793 AN: 151990 Hom.: 22423 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.532 AC: 80866 AN: 152108 Hom.: 22454 Cov.: 33 AF XY: 0.531 AC XY: 39510 AN XY: 74348

African (AFR) AF: 0.353 AC: 14661 AN: 41488

American (AMR) AF: 0.629 AC: 9608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3472

East Asian (EAS) AF: 0.568 AC: 2941 AN: 5176

South Asian (SAS) AF: 0.536 AC: 2584 AN: 4822

European-Finnish (FIN) AF: 0.582 AC: 6155 AN: 10574

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41044 AN: 67978

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.583 Hom.: 13317

Bravo AF: 0.529

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	18
DANN	Benign	0.64
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs4813709; hg19: chr20-4619157;