rs404409

Variant names:

• chr4-176516942-A-G
• rs404409
• ENST00000752489.1:n.172-3362A>G

Variant summary

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

The ENST00000752489.1(ENSG00000298014):​n.172-3362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,530 control chromosomes in the GnomAD database, including 26,237 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 0.59 (26237 hom., cov: 30)
• Consequence: ENSG00000298014 ENST00000752489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 1 publications found

Genes affected

ENSG00000298014 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900817	XR_007058376.1	n.1158-3362A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298014	ENST00000752489.1	n.172-3362A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88714 AN: 151414 Hom.: 26204 Cov.: 30

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.586 AC: 88798 AN: 151530 Hom.: 26237 Cov.: 30 AF XY: 0.585 AC XY: 43313 AN XY: 74014

African (AFR) AF: 0.653 AC: 26939 AN: 41250

American (AMR) AF: 0.577 AC: 8796 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3466

East Asian (EAS) AF: 0.408 AC: 2103 AN: 5152

South Asian (SAS) AF: 0.590 AC: 2834 AN: 4802

European-Finnish (FIN) AF: 0.569 AC: 5941 AN: 10438

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38533 AN: 67876

Other (OTH) AF: 0.596 AC: 1253 AN: 2104

Alfa AF: 0.604 Hom.: 3569

Bravo AF: 0.584

Asia WGS AF: 0.506 AC: 1757 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs404409; hg19: chr4-177438093;