2-144602342-C-T

Variant names:

• chr2-144602342-C-T
• rs10496964
• ENST00000813801.1:n.204-25970C>T

Variant summary

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

The ENST00000813801.1(LINC01412):​n.204-25970C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,052 control chromosomes in the GnomAD database, including 1,536 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 0.13 (1536 hom., cov: 30)
• Consequence: LINC01412 ENST00000813801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906
• Publications: 16 publications found

Genes affected

LINC01412 (HGNC:50704): (long intergenic non-protein coding RNA 1412)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 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
LINC01412	ENST00000813801.1	n.204-25970C>T		intron_variant	Intron 2 of 2
LINC01412	ENST00000813811.1	n.415+18843C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19330 AN: 151934 Hom.: 1540 Cov.: 30

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.127 AC: 19324 AN: 152052 Hom.: 1536 Cov.: 30 AF XY: 0.131 AC XY: 9772 AN XY: 74346

African (AFR) AF: 0.0376 AC: 1562 AN: 41508

American (AMR) AF: 0.112 AC: 1714 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.168 AC: 868 AN: 5166

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4808

European-Finnish (FIN) AF: 0.185 AC: 1953 AN: 10560

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11272 AN: 67944

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.142 Hom.: 3312

Bravo AF: 0.113

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.65
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs10496964; hg19: chr2-145359909;