12-67464073-C-T

Variant names:

• chr12-67464073-C-T
• rs2700565
• ENST00000650195.1:n.153+11902C>T

Variant summary

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

The ENST00000650195.1(LINC02408):​n.153+11902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,086 control chromosomes in the GnomAD database, including 54,664 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 0.85 (54664 hom., cov: 31)
• Consequence: LINC02408 ENST00000650195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 2 publications found

Genes affected

LINC02408 (HGNC:53337): (long intergenic non-protein coding RNA 2408)

LOC105369812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650195.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02408	ENST00000650195.1		n.153+11902C>T		intron	N/A
	LINC02408	ENST00000774321.1		n.105+11902C>T		intron	N/A
	LINC02408	ENST00000774322.1		n.121+11902C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128524 AN: 151968 Hom.: 54596 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.846 AC: 128651 AN: 152086 Hom.: 54664 Cov.: 31 AF XY: 0.843 AC XY: 62662 AN XY: 74324

African (AFR) AF: 0.910 AC: 37767 AN: 41490

American (AMR) AF: 0.883 AC: 13481 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3470

East Asian (EAS) AF: 0.840 AC: 4342 AN: 5168

South Asian (SAS) AF: 0.775 AC: 3731 AN: 4812

European-Finnish (FIN) AF: 0.773 AC: 8165 AN: 10568

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55531 AN: 67986

Other (OTH) AF: 0.862 AC: 1823 AN: 2114

Alfa AF: 0.824 Hom.: 91124

Bravo AF: 0.861

Asia WGS AF: 0.821 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.17
PhyloP100		-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2700565;

hg19: chr12-67857853;