9-93323088-C-T

Position:

• chr9-93323088-C-T

Variant summary

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

The ENST00000648864.1(ENSG00000290685):​n.730-3914G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 121,666 control chromosomes in the GnomAD database, including 13,561 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 0.48 (13561 hom., cov: 32)
• Consequence: ENST00000648864.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648864.1	n.730-3914G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.476 AC: 57864 AN: 121580 Hom.: 13558 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.476 AC: 57862 AN: 121666 Hom.: 13561 Cov.: 32 AF XY: 0.476 AC XY: 27975 AN XY: 58766

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.485

Alfa AF: 0.457 Hom.: 3022

Bravo AF: 0.380

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3001450; hg19: chr9-96085370;