2-234690308-C-T

Position:

• chr2-234690308-C-T

Variant summary

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

The NR_132376.1(LINC01173):​n.102-5341C>T 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 0.431 in 151,880 control chromosomes in the GnomAD database, including 14,646 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 0.43 (14646 hom., cov: 31)
• Consequence: LINC01173 NR_132376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

LINC01173 (HGNC:49545): (long intergenic non-protein coding RNA 1173)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01173	NR_132376.1	n.102-5341C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01173	ENST00000629370.1	n.102-5341C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65375 AN: 151762 Hom.: 14644 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.431 AC: 65406 AN: 151880 Hom.: 14646 Cov.: 31 AF XY: 0.436 AC XY: 32358 AN XY: 74228

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.432

Alfa AF: 0.456 Hom.: 7855

Bravo AF: 0.417

Asia WGS AF: 0.436 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.045
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663158; hg19: chr2-235598952;