rs968477

Variant names:

• chr9-129479582-G-A
• rs968477
• ENST00000653047.1:n.214+2423G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-129479582-G-A
• chr9-129479582-G-T

Variant summary

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

The ENST00000653047.1(LINC00963):​n.214+2423G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,146 control chromosomes in the GnomAD database, including 6,119 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 0.28 (6119 hom., cov: 33)
• Consequence: LINC00963 ENST00000653047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 6 publications found

Genes affected

LINC00963 (HGNC:48716): (long intergenic non-protein coding RNA 963)

ENSG00000309757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653047.1. 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
	LINC00963	ENST00000653047.1		n.214+2423G>A		intron	N/A
	ENSG00000309757	ENST00000843717.1		n.85-1956C>T		intron	N/A
	ENSG00000309757	ENST00000843718.1		n.188-1956C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41908 AN: 152030 Hom.: 6106 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.276 AC: 41941 AN: 152146 Hom.: 6119 Cov.: 33 AF XY: 0.279 AC XY: 20753 AN XY: 74370

African (AFR) AF: 0.226 AC: 9388 AN: 41514

American (AMR) AF: 0.319 AC: 4879 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2893 AN: 5168

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3244 AN: 10584

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18388 AN: 67998

Other (OTH) AF: 0.278 AC: 587 AN: 2112

Alfa AF: 0.270 Hom.: 15882

Bravo AF: 0.278

Asia WGS AF: 0.421 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.018
DANN	Benign	0.89
PhyloP100		-1.4

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: rs968477;

hg19: chr9-132241861;

COSMIC: COSV71994980;