chr10-99530544-T-C

Variant names:

• chr10-99530544-T-C
• rs6584283
• ENST00000548010.2:n.243+468A>G

Variant summary

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

The ENST00000548010.2(LINC01475):​n.243+468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,958 control chromosomes in the GnomAD database, including 24,242 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 0.56 (24242 hom., cov: 32)
• Consequence: LINC01475 ENST00000548010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 49 publications found

Genes affected

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

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 (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548010.2. 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
	LINC01475	NR_120618.1		n.166+468A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01475	ENST00000548010.2	TSL:1	n.243+468A>G		intron	N/A
	LINC01475	ENST00000795233.1		n.199-1860A>G		intron	N/A
	LINC01475	ENST00000795234.1		n.213-1860A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85436 AN: 151840 Hom.: 24209 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.563 AC: 85520 AN: 151958 Hom.: 24242 Cov.: 32 AF XY: 0.564 AC XY: 41870 AN XY: 74260

African (AFR) AF: 0.615 AC: 25496 AN: 41466

American (AMR) AF: 0.586 AC: 8963 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1628 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2831 AN: 5132

South Asian (SAS) AF: 0.635 AC: 3058 AN: 4812

European-Finnish (FIN) AF: 0.529 AC: 5582 AN: 10550

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.534 AC: 36279 AN: 67930

Other (OTH) AF: 0.525 AC: 1106 AN: 2106

Alfa AF: 0.543 Hom.: 70178

Bravo AF: 0.566

Asia WGS AF: 0.608 AC: 2114 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	6.2
DANN	Benign	0.63
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6584283; hg19: chr10-101290301; COSMIC: COSV60728452;