2-234692420-T-G

Variant summary

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

The NR_132376.1(LINC01173):n.102-3229T>G 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 0.751 in 152,048 control chromosomes in the GnomAD database, including 43,172 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 0.75 (43172 hom., cov: 31)
• Consequence: LINC01173 NR_132376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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 (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01173	NR_132376.1	n.102-3229T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01173	ENST00000629370.1	n.102-3229T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114094 AN: 151930 Hom.: 43126 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.751 AC: 114204 AN: 152048 Hom.: 43172 Cov.: 31 AF XY: 0.757 AC XY: 56257 AN XY: 74346

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.770

Alfa AF: 0.721 Hom.: 37642

Bravo AF: 0.751

Asia WGS AF: 0.869 AC: 3020 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	3.8
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663476; hg19: chr2-235601064;