chrX-5656287-A-G

Variant names:

• chrX-5656287-A-G
• rs5961794
• ENST00000422914.2:n.599-2584T>C

Variant summary

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

The ENST00000422914.2(LINC03070):​n.599-2584T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 1 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=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03070	ENST00000422914.2	n.599-2584T>C		intron_variant	Intron 2 of 2	3
LINC03070	ENST00000444185.5	n.346-2584T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 29940 AN: 110651 Hom.: 3012 Cov.: 23

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

African (AFR) AF: 0.259 AC: 7881 AN: 30420

American (AMR) AF: 0.184 AC: 1929 AN: 10472

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 834 AN: 2644

East Asian (EAS) AF: 0.152 AC: 532 AN: 3492

South Asian (SAS) AF: 0.434 AC: 1112 AN: 2562

European-Finnish (FIN) AF: 0.232 AC: 1358 AN: 5852

Middle Eastern (MID) AF: 0.455 AC: 96 AN: 211

European-Non Finnish (NFE) AF: 0.296 AC: 15648 AN: 52865

Other (OTH) AF: 0.298 AC: 449 AN: 1507

Alfa AF: 0.286 Hom.: 23673

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs5961794; hg19: chrX-5574328;