5-7155499-C-T

Variant names:

• chr5-7155499-C-T
• rs4702435
• ENST00000512838.2:n.426+4471C>T

Variant summary

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

The ENST00000512838.2(LINC02196):​n.426+4471C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 151,878 control chromosomes in the GnomAD database, including 56,411 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 0.86 (56411 hom., cov: 30)
• Consequence: LINC02196 ENST00000512838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

ENSG00000308577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 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
LINC02196	ENST00000512838.2	n.426+4471C>T		intron_variant	Intron 4 of 6	4
LINC02196	ENST00000648809.1	n.719+4471C>T		intron_variant	Intron 5 of 5
LINC02196	ENST00000651243.2	n.379+4471C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130658 AN: 151760 Hom.: 56360 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.861 AC: 130767 AN: 151878 Hom.: 56411 Cov.: 30 AF XY: 0.862 AC XY: 63970 AN XY: 74228

African (AFR) AF: 0.839 AC: 34753 AN: 41436

American (AMR) AF: 0.868 AC: 13219 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2700 AN: 3464

East Asian (EAS) AF: 0.809 AC: 4159 AN: 5144

South Asian (SAS) AF: 0.800 AC: 3847 AN: 4806

European-Finnish (FIN) AF: 0.912 AC: 9657 AN: 10590

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59651 AN: 67896

Other (OTH) AF: 0.860 AC: 1812 AN: 2108

Alfa AF: 0.866 Hom.: 92074

Bravo AF: 0.857

Asia WGS AF: 0.793 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4702435; hg19: chr5-7155612;