rs2128519

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-5698923-A-G
• chrX-5698923-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC03070	ENST00000422914.2	n.397+27007T>C		intron_variant	Intron 1 of 2	3
LINC03070	ENST00000444185.5	n.28+27007T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.454 AC: 49866 AN: 109840 Hom.: 8489 Cov.: 22 AF XY: 0.446 AC XY: 14333 AN XY: 32134

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

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.463

Alfa AF: 0.384 Hom.: 7825

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
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: rs2128519; hg19: chrX-5616964;