9-30209423-C-T

Variant names:

• chr9-30209423-C-T
• rs4879416
• ENST00000761398.1:n.335-3599G>A

Variant summary

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

The ENST00000761398.1(ENSG00000299168):​n.335-3599G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 151,910 control chromosomes in the GnomAD database, including 52,951 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 0.83 (52951 hom., cov: 30)
• Consequence: ENSG00000299168 ENST00000761398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 1 publications found

Genes affected

ENSG00000299168 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761398.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299168	ENST00000761398.1		n.335-3599G>A		intron	N/A
	ENSG00000299168	ENST00000761399.1		n.454-3599G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125724 AN: 151792 Hom.: 52927 Cov.: 30

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.828 AC: 125805 AN: 151910 Hom.: 52951 Cov.: 30 AF XY: 0.831 AC XY: 61680 AN XY: 74252

African (AFR) AF: 0.659 AC: 27270 AN: 41388

American (AMR) AF: 0.853 AC: 12996 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3196 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4604 AN: 5132

South Asian (SAS) AF: 0.802 AC: 3860 AN: 4812

European-Finnish (FIN) AF: 0.945 AC: 10014 AN: 10596

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60954 AN: 67958

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.873 Hom.: 41882

Bravo AF: 0.816

Asia WGS AF: 0.845 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.48
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs4879416; hg19: chr9-30209421;