rs10507005

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 ENST00000546710.2(LINC02404):​n.99+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 ENST00000546710.2 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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02404	XR_945199.3	n.248+169T>C		intron_variant	Intron 2 of 2
LINC02404	XR_945201.2	n.199+169T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02404	ENST00000546710.2	n.99+169T>C		intron_variant	Intron 1 of 1	5
LINC02404	ENST00000668890.1	n.449+169T>C		intron_variant	Intron 2 of 2
LINC02404	ENST00000801876.1	n.249+169T>C		intron_variant	Intron 2 of 2
LINC02404	ENST00000801877.1	n.552+169T>C		intron_variant	Intron 3 of 3

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 v4.3

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;