rs11265930

Variant names:

• chr9-89765957-A-C
• rs11265930
• ENST00000718835.1:n.816-55294A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-89765957-A-C
• chr9-89765957-A-T

Variant summary

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

The ENST00000718835.1(LINC03062):​n.816-55294A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,234 control chromosomes in the GnomAD database, including 492 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 0.071 (492 hom., cov: 32)
• Consequence: LINC03062 ENST00000718835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 publications found

Genes affected

LINC03062 (HGNC:56369): (long intergenic non-protein coding RNA 3062)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03062	ENST00000718835.1	n.816-55294A>C		intron_variant	Intron 5 of 5
LINC03062	ENST00000718836.1	n.376-55294A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10738 AN: 152116 Hom.: 492 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0705 AC: 10739 AN: 152234 Hom.: 492 Cov.: 32 AF XY: 0.0690 AC XY: 5138 AN XY: 74432

African (AFR) AF: 0.0178 AC: 741 AN: 41548

American (AMR) AF: 0.0598 AC: 915 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0750 AC: 362 AN: 4824

European-Finnish (FIN) AF: 0.0621 AC: 658 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7266 AN: 68004

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0940 Hom.: 871

Bravo AF: 0.0655

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.50
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11265930; hg19: chr9-92467404;