rs5961794

Positions:

• chrX-5656287-A-G
• chrX-5656287-A-T

Variant summary

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

The ENST00000422914.2(LINC03070):​n.599-2584T>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 0.271 in 110,704 control chromosomes in the GnomAD database, including 3,011 homozygotes. There are 8,686 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 0.27 (3011 hom., 8686 hem., cov: 23)
• Consequence: LINC03070 ENST00000422914.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03070	ENST00000422914.2	n.599-2584T>C		intron_variant, non_coding_transcript_variant		3
LINC03070	ENST00000444185.5	n.346-2584T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 29940 AN: 110651 Hom.: 3012 Cov.: 23 AF XY: 0.263 AC XY: 8657 AN XY: 32925

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.271 AC: 29961 AN: 110704 Hom.: 3011 Cov.: 23 AF XY: 0.263 AC XY: 8686 AN XY: 32988

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.298

Alfa AF: 0.293 Hom.: 17551

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961794; hg19: chrX-5574328;