rs982463

Variant names:

• chr9-115744712-C-A
• rs982463
• ENST00000832032.1:n.322-3150G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-115744712-C-A
• chr9-115744712-C-G
• chr9-115744712-C-T

Variant summary

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

The ENST00000832032.1(ENSG00000228714):​n.322-3150G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,214 control chromosomes in the GnomAD database, including 387 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 0.066 (387 hom., cov: 32)
• Consequence: ENSG00000228714 ENST00000832032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 1 publications found

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228714	ENST00000832032.1		n.322-3150G>T		intron	N/A
	ENSG00000308189	ENST00000832372.1		n.206+607C>A		intron	N/A
	ENSG00000308189	ENST00000832373.1		n.235+607C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9967 AN: 152096 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0225

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0656 AC: 9985 AN: 152214 Hom.: 387 Cov.: 32 AF XY: 0.0652 AC XY: 4851 AN XY: 74416

African (AFR) AF: 0.0888 AC: 3690 AN: 41534

American (AMR) AF: 0.0843 AC: 1288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4830

European-Finnish (FIN) AF: 0.0683 AC: 724 AN: 10604

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0564 AC: 3834 AN: 68014

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0178 Hom.: 12

Bravo AF: 0.0699

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs982463;

hg19: chr9-118506991;