X-5698923-A-G

Variant names:

• chrX-5698923-A-G
• rs2128519
• ENST00000422914.2:n.397+27007T>C

Variant summary

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

The ENST00000422914.2(LINC03070):​n.397+27007T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 109,897 control chromosomes in the GnomAD database, including 8,483 homozygotes. There are 14,374 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 0.45 (8483 hom., 14374 hem., cov: 22)
• Consequence: LINC03070 ENST00000422914.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 publications found

Genes affected

LINC03070 (HGNC:56642): (long intergenic non-protein coding RNA 3070)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422914.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03070	ENST00000422914.2	TSL:3	n.397+27007T>C		intron	N/A
	LINC03070	ENST00000444185.5	TSL:3	n.28+27007T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 49866 AN: 109840 Hom.: 8489 Cov.: 22

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.454 AC: 49899 AN: 109897 Hom.: 8483 Cov.: 22 AF XY: 0.446 AC XY: 14374 AN XY: 32201

African (AFR) AF: 0.559 AC: 16865 AN: 30148

American (AMR) AF: 0.361 AC: 3714 AN: 10295

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1235 AN: 2624

East Asian (EAS) AF: 0.693 AC: 2362 AN: 3410

South Asian (SAS) AF: 0.527 AC: 1336 AN: 2537

European-Finnish (FIN) AF: 0.397 AC: 2296 AN: 5789

Middle Eastern (MID) AF: 0.522 AC: 109 AN: 209

European-Non Finnish (NFE) AF: 0.402 AC: 21164 AN: 52698

Other (OTH) AF: 0.463 AC: 697 AN: 1506

Alfa AF: 0.402 Hom.: 12849

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs2128519; hg19: chrX-5616964;