ENST00000797390.1:n.166+5572A>G

Variant names:

• chr3-45075681-A-G
• rs6773576
• ENST00000797390.1:n.166+5572A>G

Variant summary

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

The ENST00000797390.1(ENSG00000303828):​n.166+5572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,016 control chromosomes in the GnomAD database, including 48,963 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 0.80 (48963 hom., cov: 31)
• Consequence: ENSG00000303828 ENST00000797390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 5 publications found

Genes affected

ENSG00000303828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906233	XR_007095897.1	n.274+5572A>G		intron_variant	Intron 2 of 3
LOC124906233	XR_007095898.1	n.188-5972A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303828	ENST00000797390.1	n.166+5572A>G		intron_variant	Intron 2 of 3
ENSG00000303828	ENST00000797391.1	n.159+5572A>G		intron_variant	Intron 2 of 2
ENSG00000303828	ENST00000797392.1	n.152+5572A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121823 AN: 151898 Hom.: 48918 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.802 AC: 121922 AN: 152016 Hom.: 48963 Cov.: 31 AF XY: 0.803 AC XY: 59683 AN XY: 74288

African (AFR) AF: 0.758 AC: 31371 AN: 41410

American (AMR) AF: 0.821 AC: 12534 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3470

East Asian (EAS) AF: 0.918 AC: 4748 AN: 5174

South Asian (SAS) AF: 0.893 AC: 4304 AN: 4822

European-Finnish (FIN) AF: 0.793 AC: 8384 AN: 10568

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54834 AN: 67994

Other (OTH) AF: 0.817 AC: 1722 AN: 2108

Alfa AF: 0.811 Hom.: 37420

Bravo AF: 0.804

Asia WGS AF: 0.863 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6773576; hg19: chr3-45117173;