chrX-63405319-G-T

Variant names:

• chrX-63405319-G-T
• rs10127000
• ENST00000608788.7:n.255-5416C>A

Variant summary

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

The ENST00000610088.6(LINC01278):​n.369-5416C>A variant causes a intron 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 ENST00000610088.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610088.6. 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
	LINC01278	ENST00000608788.7	TSL:5	n.255-5416C>A		intron	N/A
	LINC01278	ENST00000610088.6	TSL:4	n.369-5416C>A		intron	N/A
	LINC01278	ENST00000610234.5	TSL:4	n.350-5416C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 21228 AN: 111449 Hom.: 4070 Cov.: 23

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

African (AFR) AF: 0.597 AC: 18214 AN: 30518

American (AMR) AF: 0.0871 AC: 921 AN: 10572

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 112 AN: 2640

East Asian (EAS) AF: 0.00 AC: 0 AN: 3561

South Asian (SAS) AF: 0.0602 AC: 161 AN: 2674

European-Finnish (FIN) AF: 0.0103 AC: 62 AN: 6019

Middle Eastern (MID) AF: 0.0876 AC: 19 AN: 217

European-Non Finnish (NFE) AF: 0.0283 AC: 1502 AN: 53095

Other (OTH) AF: 0.168 AC: 256 AN: 1524

Alfa AF: 0.0813 Hom.: 2321

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10127000; hg19: chrX-62625199;