3-30461528-A-G

Variant names:

• chr3-30461528-A-G
• rs4613502
• ENST00000691186.1:n.213-7505A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691186.1(ENSG00000289450):​n.213-7505A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,978 control chromosomes in the GnomAD database, including 32,816 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 0.64 (32816 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000691186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_001740627.2	n.213-7505A>G		intron_variant	Intron 3 of 3
LOC101927995	XR_001740628.2	n.261-7505A>G		intron_variant	Intron 4 of 4
LOC101927995	XR_007095856.1	n.257-7505A>G		intron_variant	Intron 4 of 4
LOC105377013	XR_940683.2	n.60+5585T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289450	ENST00000691186.1	n.213-7505A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96465 AN: 151858 Hom.: 32762 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.636 AC: 96585 AN: 151978 Hom.: 32816 Cov.: 32 AF XY: 0.638 AC XY: 47384 AN XY: 74280

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.596

Alfa AF: 0.542 Hom.: 22679

Bravo AF: 0.645

Asia WGS AF: 0.817 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4613502; hg19: chr3-30503020;