chr10-99524480-T-G

Variant names:

• chr10-99524480-T-G
• rs4409764
• ENST00000548010.2:n.844-850A>C

Variant summary

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

The ENST00000548010.2(LINC01475):​n.844-850A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,868 control chromosomes in the GnomAD database, including 19,411 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 0.50 (19411 hom., cov: 31)
• Consequence: LINC01475 ENST00000548010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 72 publications found

Genes affected

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

ENSG00000228778 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01475	ENST00000548010.2	TSL:1	n.844-850A>C		intron	N/A
	LINC01475	ENST00000795235.1		n.334-850A>C		intron	N/A
	LINC01475	ENST00000795236.1		n.460-762A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76237 AN: 151750 Hom.: 19387 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.502 AC: 76300 AN: 151868 Hom.: 19411 Cov.: 31 AF XY: 0.506 AC XY: 37561 AN XY: 74206

African (AFR) AF: 0.441 AC: 18246 AN: 41376

American (AMR) AF: 0.558 AC: 8525 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2842 AN: 5148

South Asian (SAS) AF: 0.627 AC: 3017 AN: 4810

European-Finnish (FIN) AF: 0.511 AC: 5387 AN: 10532

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35098 AN: 67932

Other (OTH) AF: 0.483 AC: 1016 AN: 2104

Alfa AF: 0.509 Hom.: 73762

Bravo AF: 0.501

Asia WGS AF: 0.594 AC: 2064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.44
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4409764; hg19: chr10-101284237;