rs4838320

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000232413 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000232413	ENST00000441473.1	n.235+11004T>C		intron_variant	Intron 1 of 1	5

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

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.902

Alfa AF: 0.903 Hom.: 125320

Bravo AF: 0.883

Asia WGS AF: 0.893 AC: 3106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4838320; hg19: chr9-128831097;