chr3-30438593-C-T

Variant names:

• chr3-30438593-C-T
• rs6790925
• ENST00000691186.2:n.282-30440C>T

Variant summary

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

The ENST00000691186.2(ENSG00000289450):​n.282-30440C>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 ENST00000691186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 18 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691186.2. 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
	ENSG00000289450	ENST00000691186.2		n.282-30440C>T		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.399-16227G>A		intron	N/A
	ENSG00000289450	ENST00000813894.1		n.392-30440C>T		intron	N/A

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

African (AFR) AF: 0.382 AC: 15822 AN: 41406

American (AMR) AF: 0.324 AC: 4938 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2818 AN: 5128

South Asian (SAS) AF: 0.409 AC: 1963 AN: 4798

European-Finnish (FIN) AF: 0.408 AC: 4296 AN: 10534

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24553 AN: 67934

Other (OTH) AF: 0.360 AC: 761 AN: 2112

Alfa AF: 0.360 Hom.: 19117

Bravo AF: 0.369

Asia WGS AF: 0.484 AC: 1682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.069
DANN	Benign	0.44
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs6790925; hg19: chr3-30480085;