9-122403515-C-T

Variant names:

• chr9-122403515-C-T
• rs4837963
• ENST00000433572.3:n.50+59C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433572.3(ENSG00000234156):​n.50+59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 151,980 control chromosomes in the GnomAD database, including 758 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 0.087 (758 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000234156 ENST00000433572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

Genes affected

ENSG00000234156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902264	XR_007061758.1	n.-220G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000433572.3	n.50+59C>T		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13233 AN: 151862 Hom.: 749 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0896

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0872 AC: 13254 AN: 151980 Hom.: 758 Cov.: 32 AF XY: 0.0878 AC XY: 6519 AN XY: 74242

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0712 Hom.: 113

Bravo AF: 0.0876

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837963; hg19: chr9-125165794;