chr9-13469834-G-A

Variant names:

• chr9-13469834-G-A
• rs9298688
• ENST00000428006.4:n.274-17269G>A

Variant summary

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

The ENST00000428006.4(ENSG00000226197):​n.274-17269G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,982 control chromosomes in the GnomAD database, including 9,505 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 0.35 (9505 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000428006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 2 publications found

Genes affected

ENSG00000226197 (HGNC:):

LINC01235 (HGNC:49769): (long intergenic non-protein coding RNA 1235)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428006.4. 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
	ENSG00000226197	ENST00000428006.4	TSL:2	n.274-17269G>A		intron	N/A
	ENSG00000226197	ENST00000664438.1		n.112+23241G>A		intron	N/A
	ENSG00000226197	ENST00000664575.2		n.328-17269G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53303 AN: 151864 Hom.: 9504 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.351 AC: 53335 AN: 151982 Hom.: 9505 Cov.: 32 AF XY: 0.351 AC XY: 26075 AN XY: 74294

African (AFR) AF: 0.347 AC: 14376 AN: 41444

American (AMR) AF: 0.354 AC: 5407 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2486 AN: 5156

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10576

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23294 AN: 67932

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.194 Hom.: 399

Bravo AF: 0.356

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.59
PhyloP100		-2.0

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: rs9298688;

hg19: chr9-13469833;