rs4838320

Variant names:

• chr9-126068818-T-C
• rs4838320
• ENST00000441473.1:n.235+11004T>C

Variant summary

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

The ENST00000441473.1(ENSG00000232413):​n.235+11004T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,324 control chromosomes in the GnomAD database, including 59,245 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 0.88 (59245 hom., cov: 35)
• Consequence: ENSG00000232413 ENST00000441473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 6 publications found

Genes affected

ENSG00000232413 (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 (AMR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441473.1. 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
	ENSG00000232413	ENST00000441473.1	TSL:5	n.235+11004T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134046 AN: 152206 Hom.: 59203 Cov.: 35

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.881 AC: 134145 AN: 152324 Hom.: 59245 Cov.: 35 AF XY: 0.881 AC XY: 65581 AN XY: 74476

African (AFR) AF: 0.816 AC: 33893 AN: 41558

American (AMR) AF: 0.926 AC: 14177 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3042 AN: 3472

East Asian (EAS) AF: 0.893 AC: 4631 AN: 5184

South Asian (SAS) AF: 0.857 AC: 4145 AN: 4834

European-Finnish (FIN) AF: 0.908 AC: 9644 AN: 10620

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61608 AN: 68028

Other (OTH) AF: 0.902 AC: 1909 AN: 2116

Alfa AF: 0.899 Hom.: 257768

Bravo AF: 0.883

Asia WGS AF: 0.893 AC: 3106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.23
PhyloP100		-1.5

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: rs4838320;

hg19: chr9-128831097;