3-153935638-T-C

Variant names:

• chr3-153935638-T-C
• rs10935960
• ENST00000463297.1:n.209+578T>C

Variant summary

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

The ENST00000488210.1(LINC02006):​n.420+1870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,874 control chromosomes in the GnomAD database, including 31,729 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 0.63 (31729 hom., cov: 31)
• Consequence: LINC02006 ENST00000488210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 1 publications found

Genes affected

ENSG00000243486 (HGNC:):

LINC02006 (HGNC:52842): (long intergenic non-protein coding RNA 2006)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488210.1. 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
	ENSG00000243486	ENST00000463297.1	TSL:5	n.209+578T>C		intron	N/A
	LINC02006	ENST00000488210.1	TSL:4	n.420+1870A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96012 AN: 151756 Hom.: 31728 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.632 AC: 96045 AN: 151874 Hom.: 31729 Cov.: 31 AF XY: 0.636 AC XY: 47221 AN XY: 74206

African (AFR) AF: 0.422 AC: 17477 AN: 41390

American (AMR) AF: 0.720 AC: 10980 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2318 AN: 3466

East Asian (EAS) AF: 0.919 AC: 4741 AN: 5160

South Asian (SAS) AF: 0.662 AC: 3182 AN: 4810

European-Finnish (FIN) AF: 0.707 AC: 7446 AN: 10530

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47688 AN: 67962

Other (OTH) AF: 0.640 AC: 1349 AN: 2108

Alfa AF: 0.678 Hom.: 26128

Bravo AF: 0.626

Asia WGS AF: 0.749 AC: 2602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.73
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10935960; hg19: chr3-153653427;