ENST00000553095.1:n.174+2570T>C

Variant names:

• chr12-95805840-T-C
• rs1369822
• ENST00000553095.2:n.193+2570T>C

Variant summary

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

The ENST00000553095.2(LINC02410):​n.193+2570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,030 control chromosomes in the GnomAD database, including 32,390 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 0.63 (32390 hom., cov: 31)
• Consequence: LINC02410 ENST00000553095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 publications found

Genes affected

LINC02410 (HGNC:53339): (long intergenic non-protein coding RNA 2410)

SNRPF-DT (HGNC:55452): (SNRPF divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553095.2. 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
	SNRPF-DT	NR_135014.1		n.155-10183A>G		intron	N/A
	LINC02410	NR_135016.1		n.174+2570T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02410	ENST00000553095.2	TSL:2	n.193+2570T>C		intron	N/A
	SNRPF-DT	ENST00000553194.1	TSL:3	n.155-10183A>G		intron	N/A
	SNRPF-DT	ENST00000670743.2		n.166-10183A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96112 AN: 151912 Hom.: 32333 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.633 AC: 96222 AN: 152030 Hom.: 32390 Cov.: 31 AF XY: 0.639 AC XY: 47494 AN XY: 74290

African (AFR) AF: 0.855 AC: 35440 AN: 41474

American (AMR) AF: 0.622 AC: 9497 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3466

East Asian (EAS) AF: 0.872 AC: 4514 AN: 5174

South Asian (SAS) AF: 0.616 AC: 2967 AN: 4820

European-Finnish (FIN) AF: 0.630 AC: 6655 AN: 10562

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33710 AN: 67962

Other (OTH) AF: 0.612 AC: 1291 AN: 2110

Alfa AF: 0.535 Hom.: 12731

Bravo AF: 0.641

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1369822; hg19: chr12-96199618;