rs9380516

Variant names:

• chr6-35534425-T-C
• rs9380516
• ENST00000722033.1:n.122-10443T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-35534425-T-C
• chr6-35534425-T-G

Variant summary

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

The ENST00000722033.1(LINC03135):​n.122-10443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 151,958 control chromosomes in the GnomAD database, including 54,794 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 0.85 (54794 hom., cov: 30)
• Consequence: LINC03135 ENST00000722033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 16 publications found

Genes affected

LINC03135 (HGNC:58100):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722033.1. 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
	LINC03135	ENST00000722033.1		n.122-10443T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.849 AC: 128853 AN: 151840 Hom.: 54743 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.849 AC: 128968 AN: 151958 Hom.: 54794 Cov.: 30 AF XY: 0.847 AC XY: 62898 AN XY: 74270

African (AFR) AF: 0.877 AC: 36324 AN: 41402

American (AMR) AF: 0.868 AC: 13231 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4373 AN: 5168

South Asian (SAS) AF: 0.763 AC: 3671 AN: 4814

European-Finnish (FIN) AF: 0.817 AC: 8633 AN: 10566

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57151 AN: 67980

Other (OTH) AF: 0.827 AC: 1744 AN: 2110

Alfa AF: 0.844 Hom.: 109265

Bravo AF: 0.856

Asia WGS AF: 0.819 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		0.30

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: rs9380516;

hg19: chr6-35502202;