ENST00000797583.1:n.369-23864G>A

Variant names:

• chr5-30814523-C-T
• rs2330607
• ENST00000797583.1:n.369-23864G>A

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.369-23864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,978 control chromosomes in the GnomAD database, including 44,772 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 0.77 (44772 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 3 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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
ENSG00000303861	ENST00000797583.1	n.369-23864G>A		intron_variant	Intron 4 of 4
ENSG00000303861	ENST00000797584.1	n.277-23864G>A		intron_variant	Intron 1 of 2
ENSG00000303861	ENST00000797585.1	n.184-23864G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116368 AN: 151860 Hom.: 44730 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.766 AC: 116463 AN: 151978 Hom.: 44772 Cov.: 32 AF XY: 0.765 AC XY: 56824 AN XY: 74280

African (AFR) AF: 0.795 AC: 32997 AN: 41484

American (AMR) AF: 0.743 AC: 11353 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3162 AN: 5128

South Asian (SAS) AF: 0.742 AC: 3571 AN: 4814

European-Finnish (FIN) AF: 0.727 AC: 7645 AN: 10510

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52534 AN: 67978

Other (OTH) AF: 0.771 AC: 1629 AN: 2114

Alfa AF: 0.758 Hom.: 8103

Bravo AF: 0.768

Asia WGS AF: 0.727 AC: 2529 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	1.7
DANN	Benign	0.39
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2330607; hg19: chr5-30814630;