X-51178144-T-G

Variant names:

• chrX-51178144-T-G
• rs6614655
• ENST00000442994.2:n.525-6273A>C

Variant summary

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

The ENST00000442994.2(LINC01284):​n.525-6273A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 110,864 control chromosomes in the GnomAD database, including 2,552 homozygotes. There are 7,092 hemizygotes in GnomAD. 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 0.23 (2552 hom., 7092 hem., cov: 22)
• Consequence: LINC01284 ENST00000442994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 1 publications found

Genes affected

LINC01284 (HGNC:50342): (long intergenic non-protein coding RNA 1284)

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.216).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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
LINC01284	ENST00000442994.2	n.525-6273A>C		intron_variant	Intron 2 of 11	5
LINC01284	ENST00000665808.1	n.1851-6273A>C		intron_variant	Intron 2 of 4
LINC01284	ENST00000717296.1	n.749-6273A>C		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.227 AC: 25189 AN: 110818 Hom.: 2547 Cov.: 22

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0180

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.228 AC: 25230 AN: 110864 Hom.: 2552 Cov.: 22 AF XY: 0.214 AC XY: 7092 AN XY: 33110

African (AFR) AF: 0.372 AC: 11331 AN: 30430

American (AMR) AF: 0.116 AC: 1221 AN: 10501

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 336 AN: 2637

East Asian (EAS) AF: 0.0181 AC: 64 AN: 3544

South Asian (SAS) AF: 0.0871 AC: 227 AN: 2605

European-Finnish (FIN) AF: 0.237 AC: 1371 AN: 5794

Middle Eastern (MID) AF: 0.206 AC: 44 AN: 214

European-Non Finnish (NFE) AF: 0.192 AC: 10143 AN: 52956

Other (OTH) AF: 0.219 AC: 332 AN: 1514

Alfa AF: 0.219 Hom.: 1429

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.2
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6614655; hg19: -;