ENST00000798472.1:n.377-3249G>A

Variant names:

• chr5-148869255-G-A
• rs9325124
• ENST00000798472.1:n.377-3249G>A

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.377-3249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,392 control chromosomes in the GnomAD database, including 19,303 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 0.49 (19303 hom., cov: 30)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 6 publications found

Genes affected

ENSG00000303969 (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 (EAS) allele frequency at 95% confidence interval = 0.626 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
ENSG00000303969	ENST00000798472.1	n.377-3249G>A		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.350-3249G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74789 AN: 151272 Hom.: 19293 Cov.: 30

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.494 AC: 74835 AN: 151392 Hom.: 19303 Cov.: 30 AF XY: 0.494 AC XY: 36531 AN XY: 73896

African (AFR) AF: 0.629 AC: 26002 AN: 41308

American (AMR) AF: 0.519 AC: 7882 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1175 AN: 3456

East Asian (EAS) AF: 0.644 AC: 3312 AN: 5140

South Asian (SAS) AF: 0.301 AC: 1432 AN: 4764

European-Finnish (FIN) AF: 0.452 AC: 4717 AN: 10428

Middle Eastern (MID) AF: 0.417 AC: 121 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28780 AN: 67816

Other (OTH) AF: 0.463 AC: 974 AN: 2102

Alfa AF: 0.445 Hom.: 59430

Bravo AF: 0.513

Asia WGS AF: 0.463 AC: 1608 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	1.9
DANN	Benign	0.54
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9325124; hg19: chr5-148248818;