rs406589

Variant names:

• chr3-41083822-G-T
• rs406589
• ENST00000808368.1:n.939+1928C>A

Variant summary

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

The ENST00000808368.1(ENSG00000305067):​n.939+1928C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,958 control chromosomes in the GnomAD database, including 16,049 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 0.45 (16049 hom., cov: 33)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 2 publications found

Genes affected

ENSG00000305067 (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 (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305067	ENST00000808368.1	n.939+1928C>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68497 AN: 151838 Hom.: 16042 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.451 AC: 68535 AN: 151958 Hom.: 16049 Cov.: 33 AF XY: 0.458 AC XY: 34017 AN XY: 74278

African (AFR) AF: 0.383 AC: 15860 AN: 41414

American (AMR) AF: 0.537 AC: 8216 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3301 AN: 5156

South Asian (SAS) AF: 0.658 AC: 3169 AN: 4818

European-Finnish (FIN) AF: 0.408 AC: 4304 AN: 10548

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30087 AN: 67948

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.441 Hom.: 2539

Bravo AF: 0.456

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.77
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs406589; hg19: chr3-41125313;