chr4-176516942-A-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752489.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298014	ENST00000752489.1		n.172-3362A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs404409;

hg19: chr4-177438093;