chr9-86478840-C-T

Variant names:

• chr9-86478840-C-T
• rs353793
• ENST00000438582.2:n.385-9547C>T

Variant summary

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

The ENST00000438582.2(ENSG00000235819):​n.385-9547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,764 control chromosomes in the GnomAD database, including 24,170 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 0.55 (24170 hom., cov: 31)
• Consequence: ENSG00000235819 ENST00000438582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724080	XR_007061636.1	n.731-50983C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235819	ENST00000438582.2	n.385-9547C>T		intron_variant	Intron 3 of 3	5
ENSG00000235819	ENST00000657061.1	n.359-9547C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84044 AN: 151646 Hom.: 24150 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.554 AC: 84100 AN: 151764 Hom.: 24170 Cov.: 31 AF XY: 0.565 AC XY: 41898 AN XY: 74146

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.577

Alfa AF: 0.539 Hom.: 2707

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353793; hg19: chr9-89093755;