rs2128519

chrX-5698923-A-GchrX-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03070	ENST00000422914.2	n.397+27007T>C		intron_variant, non_coding_transcript_variant		3
LINC03070	ENST00000444185.5	n.28+27007T>C		intron_variant, non_coding_transcript_variant		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;