rs7705924

Variant names:

• chr5-102611094-A-G
• rs7705924
• ENST00000504436.1:n.200-6102A>G

Variant summary

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

The ENST00000504436.1(LINC00492):​n.200-6102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,232 control chromosomes in the GnomAD database, including 216 homozygotes. 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 0.050 (216 hom., cov: 32)
• Consequence: LINC00492 ENST00000504436.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926
• Publications: 17 publications found

Genes affected

LINC00492 (HGNC:43429): (long intergenic non-protein coding RNA 492)

LINC00491 (HGNC:43428): (long intergenic non-protein coding RNA 491)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00492	NR_047462.1	n.200-6102A>G		intron_variant	Intron 1 of 1
LINC00491	NR_103753.1	n.388-1328T>C		intron_variant	Intron 2 of 2
LINC00491	NR_103754.1	n.372+799T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00492	ENST00000504436.1	n.200-6102A>G		intron_variant	Intron 1 of 1	3
LINC00491	ENST00000505527.6	n.230+799T>C		intron_variant	Intron 3 of 3	3
LINC00491	ENST00000508339.2	n.591-1328T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7592 AN: 152114 Hom.: 214 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0499 AC: 7598 AN: 152232 Hom.: 216 Cov.: 32 AF XY: 0.0496 AC XY: 3690 AN XY: 74450

African (AFR) AF: 0.0690 AC: 2869 AN: 41552

American (AMR) AF: 0.0658 AC: 1006 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0156 AC: 81 AN: 5194

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4824

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0378 AC: 2572 AN: 67982

Other (OTH) AF: 0.0579 AC: 122 AN: 2106

Alfa AF: 0.0434 Hom.: 523

Bravo AF: 0.0538

Asia WGS AF: 0.0390 AC: 136 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.91
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs7705924; hg19: chr5-101946798;