ENST00000797583.1:n.368+29817C>T

Variant names:

• chr5-30845358-G-A
• rs7704530
• ENST00000797583.1:n.368+29817C>T

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.368+29817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 151,828 control chromosomes in the GnomAD database, including 43,524 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 0.75 (43524 hom., cov: 31)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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.368+29817C>T		intron_variant	Intron 4 of 4
ENSG00000303861	ENST00000797584.1	n.276+29817C>T		intron_variant	Intron 1 of 2
ENSG00000303861	ENST00000797585.1	n.183+4632C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114246 AN: 151710 Hom.: 43476 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.753 AC: 114355 AN: 151828 Hom.: 43524 Cov.: 31 AF XY: 0.752 AC XY: 55807 AN XY: 74168

African (AFR) AF: 0.848 AC: 35176 AN: 41476

American (AMR) AF: 0.740 AC: 11264 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2623 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2817 AN: 5156

South Asian (SAS) AF: 0.748 AC: 3610 AN: 4824

European-Finnish (FIN) AF: 0.702 AC: 7387 AN: 10522

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49210 AN: 67848

Other (OTH) AF: 0.742 AC: 1565 AN: 2110

Alfa AF: 0.733 Hom.: 29499

Bravo AF: 0.759

Asia WGS AF: 0.702 AC: 2439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs7704530; hg19: chr5-30845465;