rs10127000

chrX-63405319-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667050.1(LINC01278):n.285-5416C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 111,501 control chromosomes in the GnomAD database, including 4,069 homozygotes. There are 5,929 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 0.19 (4069 hom., 5929 hem., cov: 23)
• Consequence: LINC01278 ENST00000667050.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LINC01278 (HGNC:28090): (long intergenic non-protein coding RNA 1278)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01278	ENST00000667050.1	n.285-5416C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 21228 AN: 111449 Hom.: 4070 Cov.: 23 AF XY: 0.176 AC XY: 5911 AN XY: 33679

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.191 AC: 21247 AN: 111501 Hom.: 4069 Cov.: 23 AF XY: 0.176 AC XY: 5929 AN XY: 33741

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0909 Hom.: 1630

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10127000; hg19: chrX-62625199;