3-145360822-A-G

Variant names:

• chr3-145360822-A-G
• rs344971
• ENST00000749387.1:n.399-21429A>G

Variant summary

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

The ENST00000749387.1(ENSG00000297629):​n.399-21429A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 151,916 control chromosomes in the GnomAD database, including 64,768 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 0.92 (64768 hom., cov: 32)
• Consequence: ENSG00000297629 ENST00000749387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 1 publications found

Genes affected

ENSG00000297629 (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 = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297629	ENST00000749387.1		n.399-21429A>G		intron	N/A
	ENSG00000297629	ENST00000749388.1		n.298-12875A>G		intron	N/A
	ENSG00000297629	ENST00000749389.1		n.278-12363A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140131 AN: 151798 Hom.: 64712 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.923 AC: 140245 AN: 151916 Hom.: 64768 Cov.: 32 AF XY: 0.923 AC XY: 68503 AN XY: 74240

African (AFR) AF: 0.960 AC: 39854 AN: 41520

American (AMR) AF: 0.885 AC: 13450 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3134 AN: 3468

East Asian (EAS) AF: 0.956 AC: 4930 AN: 5158

South Asian (SAS) AF: 0.916 AC: 4421 AN: 4828

European-Finnish (FIN) AF: 0.926 AC: 9809 AN: 10592

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61624 AN: 67830

Other (OTH) AF: 0.919 AC: 1941 AN: 2112

Alfa AF: 0.914 Hom.: 21487

Bravo AF: 0.920

Asia WGS AF: 0.932 AC: 3232 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.67
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs344971; hg19: chr3-145078609;