chr2-234692420-T-G

Variant names:

• chr2-234692420-T-G
• rs4663476
• ENST00000629370.2:n.214-3229T>G

Variant summary

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

The ENST00000629370.2(LINC01173):​n.214-3229T>G variant causes a intron 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 ENST00000629370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01173	NR_132376.1	n.102-3229T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01173	ENST00000629370.2	n.214-3229T>G		intron_variant	Intron 1 of 3	3
LINC01173	ENST00000768858.1	n.123-3229T>G		intron_variant	Intron 1 of 3
LINC01173	ENST00000768859.1	n.100-3229T>G		intron_variant	Intron 1 of 3
LINC01173	ENST00000768860.1	n.82-3229T>G		intron_variant	Intron 1 of 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

African (AFR) AF: 0.754 AC: 31268 AN: 41452

American (AMR) AF: 0.804 AC: 12294 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2537 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4609 AN: 5170

South Asian (SAS) AF: 0.807 AC: 3886 AN: 4818

European-Finnish (FIN) AF: 0.826 AC: 8735 AN: 10576

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48313 AN: 67960

Other (OTH) AF: 0.770 AC: 1628 AN: 2114

Alfa AF: 0.728 Hom.: 77791

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
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs4663476; hg19: chr2-235601064;