3-30438593-C-T

Variant names:

• chr3-30438593-C-T
• rs6790925
• ENST00000691186.1:n.213-30440C>T

Variant summary

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

The ENST00000691186.1(ENSG00000289450):​n.213-30440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,820 control chromosomes in the GnomAD database, including 10,810 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 0.38 (10810 hom., cov: 31)
• Consequence: ENSG00000289450 ENST00000691186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_001740627.2	n.213-30440C>T		intron_variant	Intron 3 of 3
LOC101927995	XR_001740628.2	n.261-30440C>T		intron_variant	Intron 4 of 4
LOC101927995	XR_007095856.1	n.257-30440C>T		intron_variant	Intron 4 of 4
LOC105377013	XR_940683.2	n.293+2414G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289450	ENST00000691186.1	n.213-30440C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56939 AN: 151702 Hom.: 10792 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.375 AC: 56987 AN: 151820 Hom.: 10810 Cov.: 31 AF XY: 0.379 AC XY: 28094 AN XY: 74158

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.360

Alfa AF: 0.340 Hom.: 4632

Bravo AF: 0.369

Asia WGS AF: 0.484 AC: 1682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.069
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6790925; hg19: chr3-30480085;