chr5-117514223-C-T

Variant names:

• chr5-117514223-C-T
• rs374261
• ENST00000514186.5:n.365-31876C>T

Variant summary

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

The ENST00000514186.5(LINC00992):​n.365-31876C>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 ENST00000514186.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

Genes affected

LINC00992 (HGNC:48943): (long intergenic non-protein coding RNA 992)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00992	NR_046089.1	n.362-31876C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00992	ENST00000514186.5	n.365-31876C>T		intron_variant	Intron 3 of 3	5
LINC00992	ENST00000828611.1	n.302-31876C>T		intron_variant	Intron 1 of 3
LINC00992	ENST00000828612.1	n.302-12483C>T		intron_variant	Intron 1 of 3
LINC00992	ENST00000828613.1	n.527-21289C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.533 AC: 22032 AN: 41360

American (AMR) AF: 0.113 AC: 1722 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0630 AC: 218 AN: 3462

East Asian (EAS) AF: 0.0188 AC: 97 AN: 5150

South Asian (SAS) AF: 0.149 AC: 718 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10582

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7554 AN: 67630

Other (OTH) AF: 0.190 AC: 399 AN: 2102

Alfa AF: 0.202 Hom.: 810

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs374261; hg19: chr5-116849918;