2-234690308-C-T

Variant names:

• chr2-234690308-C-T
• rs4663158
• ENST00000629370.2:n.214-5341C>T

Variant summary

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

The ENST00000629370.2(LINC01173):​n.214-5341C>T variant causes a intron 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 ENST00000629370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01173	NR_132376.1	n.102-5341C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01173	ENST00000629370.2	n.214-5341C>T		intron_variant	Intron 1 of 3	3
LINC01173	ENST00000768858.1	n.123-5341C>T		intron_variant	Intron 1 of 3
LINC01173	ENST00000768859.1	n.100-5341C>T		intron_variant	Intron 1 of 3
LINC01173	ENST00000768860.1	n.81+3880C>T		intron_variant	Intron 1 of 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

African (AFR) AF: 0.313 AC: 12971 AN: 41438

American (AMR) AF: 0.489 AC: 7468 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1533 AN: 5136

South Asian (SAS) AF: 0.536 AC: 2580 AN: 4816

European-Finnish (FIN) AF: 0.603 AC: 6341 AN: 10518

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31589 AN: 67914

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.456 Hom.: 8668

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4663158; hg19: chr2-235598952;