rs7705924

Positions:

• chr5-102611094-A-G

Variant summary

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

The NR_047462.1(LINC00492):​n.200-6102A>G 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 0.0499 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 NR_047462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00492	NR_047462.1	n.200-6102A>G		intron_variant, non_coding_transcript_variant
LINC00491	NR_103756.1	n.239-1328T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00492	ENST00000504436.1	n.200-6102A>G		intron_variant, non_coding_transcript_variant		3
LINC00491	ENST00000662437.1	n.540-1328T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0378

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.0424 Hom.: 173

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705924; hg19: chr5-101946798;