chr2-144594254-T-C

Variant names:

• chr2-144594254-T-C
• rs7355746
• ENST00000813801.1:n.203+27684T>C

Variant summary

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

The ENST00000813801.1(LINC01412):​n.203+27684T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,268 control chromosomes in the GnomAD database, including 69,281 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 0.95 (69281 hom., cov: 32)
• Consequence: LINC01412 ENST00000813801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813801.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01412	ENST00000813801.1		n.203+27684T>C		intron	N/A
	LINC01412	ENST00000813811.1		n.415+10755T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144931 AN: 152150 Hom.: 69238 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.952 AC: 145028 AN: 152268 Hom.: 69281 Cov.: 32 AF XY: 0.955 AC XY: 71094 AN XY: 74468

African (AFR) AF: 0.865 AC: 35908 AN: 41504

American (AMR) AF: 0.969 AC: 14826 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3435 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5186

South Asian (SAS) AF: 0.997 AC: 4813 AN: 4826

European-Finnish (FIN) AF: 0.999 AC: 10605 AN: 10620

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67063 AN: 68034

Other (OTH) AF: 0.948 AC: 2003 AN: 2112

Alfa AF: 0.973 Hom.: 184379

Bravo AF: 0.946

Asia WGS AF: 0.989 AC: 3439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.57
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7355746; hg19: chr2-145351821;