rs374261

Positions:

• chr5-117514223-C-T

Variant summary

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

The NR_046089.1(LINC00992):​n.362-31876C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,494 control chromosomes in the GnomAD database, including 6,640 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 0.22 (6640 hom., cov: 32)
• Consequence: LINC00992 NR_046089.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

LINC00992 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00992	NR_046089.1	n.362-31876C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00992	ENST00000514186.5	n.365-31876C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33924 AN: 151376 Hom.: 6612 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0630

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.224 AC: 34001 AN: 151494 Hom.: 6640 Cov.: 32 AF XY: 0.218 AC XY: 16157 AN XY: 74060

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0630

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.190

Alfa AF: 0.192 Hom.: 712

Bravo AF: 0.237

Asia WGS AF: 0.123 AC: 428 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs374261; hg19: chr5-116849918;