rs9298688

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-13469834-G-A
• chr9-13469834-G-C
• chr9-13469834-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375977	XR_929484.3	n.490-17269G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226197	ENST00000428006.4	n.274-17269G>A		intron_variant	Intron 3 of 3	2
ENSG00000226197	ENST00000664438.1	n.112+23241G>A		intron_variant	Intron 1 of 2
ENSG00000226197	ENST00000664575.2	n.328-17269G>A		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs9298688; hg19: chr9-13469833;