chr12-91877658-T-C

Variant names:

• chr12-91877658-T-C
• rs10507005
• ENST00000546710.2:n.99+169T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000668890.1(LINC02404):​n.449+169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,334 control chromosomes in the GnomAD database, including 35 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 0.017 (35 hom., cov: 32)
• Consequence: LINC02404 ENST00000668890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 0 publications found

Genes affected

LINC02404 (HGNC:53331): (long intergenic non-protein coding RNA 2404)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.017 (2586/152334) while in subpopulation NFE AF = 0.0236 (1607/68030). AF 95% confidence interval is 0.0227. There are 35 homozygotes in GnomAd4. There are 1243 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668890.1. 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
	LINC02404	ENST00000546710.2	TSL:5	n.99+169T>C		intron	N/A
	LINC02404	ENST00000668890.1		n.449+169T>C		intron	N/A
	LINC02404	ENST00000801876.1		n.249+169T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2587 AN: 152216 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.00434

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0162

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00434

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0170 AC: 2586 AN: 152334 Hom.: 35 Cov.: 32 AF XY: 0.0167 AC XY: 1243 AN XY: 74482

African (AFR) AF: 0.00433 AC: 180 AN: 41592

American (AMR) AF: 0.0162 AC: 247 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.00414 AC: 20 AN: 4830

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1607 AN: 68030

Other (OTH) AF: 0.0156 AC: 33 AN: 2114

Alfa AF: 0.0155 Hom.: 7

Bravo AF: 0.0147

Asia WGS AF: 0.00318 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10507005; hg19: chr12-92271434;