3-45075681-A-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797390.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303828	ENST00000797390.1		n.166+5572A>G		intron	N/A
	ENSG00000303828	ENST00000797391.1		n.159+5572A>G		intron	N/A
	ENSG00000303828	ENST00000797392.1		n.152+5572A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6773576;

hg19: chr3-45117173;