5-7165151-G-T

Variant names:

• chr5-7165151-G-T
• rs17202561
• ENST00000512838.2:n.427-13841G>T

Variant summary

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

The ENST00000512838.2(LINC02196):​n.427-13841G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 152,238 control chromosomes in the GnomAD database, including 175 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 0.047 (175 hom., cov: 33)
• Consequence: LINC02196 ENST00000512838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0521 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.427-13841G>T		intron_variant	Intron 4 of 6	4
LINC02196	ENST00000648809.1	n.720-13841G>T		intron_variant	Intron 5 of 5
LINC02196	ENST00000651243.2	n.380-13841G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7139 AN: 152120 Hom.: 176 Cov.: 33

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.0647

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

GnomAD4 genome AF: 0.0469 AC: 7138 AN: 152238 Hom.: 175 Cov.: 33 AF XY: 0.0459 AC XY: 3418 AN XY: 74434

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.0403

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0430

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0444 Hom.: 133

Bravo AF: 0.0480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.080
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17202561; hg19: chr5-7165264;