9-4792339-C-T

Variant names:

• chr9-4792339-C-T
• rs423955
• ENST00000719826.1:n.295+47G>A

Variant summary

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

The ENST00000719826.1(ENSG00000293905):​n.295+47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,010 control chromosomes in the GnomAD database, including 25,910 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 0.57 (25910 hom., cov: 31)
• Consequence: ENSG00000293905 ENST00000719826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 21 publications found

Genes affected

ENSG00000293905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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
ENSG00000293905	ENST00000719826.1	n.295+47G>A		intron_variant	Intron 1 of 1
ENSG00000293905	ENST00000719827.1	n.154+183G>A		intron_variant	Intron 1 of 1
ENSG00000293905	ENST00000719828.1	n.153+183G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86350 AN: 151892 Hom.: 25909 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.568 AC: 86382 AN: 152010 Hom.: 25910 Cov.: 31 AF XY: 0.570 AC XY: 42327 AN XY: 74266

African (AFR) AF: 0.360 AC: 14917 AN: 41446

American (AMR) AF: 0.619 AC: 9457 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2042 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4038 AN: 5148

South Asian (SAS) AF: 0.542 AC: 2616 AN: 4824

European-Finnish (FIN) AF: 0.637 AC: 6711 AN: 10542

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44593 AN: 67978

Other (OTH) AF: 0.613 AC: 1297 AN: 2116

Alfa AF: 0.632 Hom.: 135353

Bravo AF: 0.563

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs423955; hg19: chr9-4792339;