2-129776708-T-C

Variant names:

• chr2-129776708-T-C
• rs7578253
• ENST00000809995.1:n.317+13211A>G

Variant summary

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

The ENST00000809995.1(LINC02572):​n.317+13211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,902 control chromosomes in the GnomAD database, including 13,449 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 0.41 (13449 hom., cov: 32)
• Consequence: LINC02572 ENST00000809995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

LINC02572 (HGNC:53634): (long intergenic non-protein coding RNA 2572)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02572	ENST00000809995.1	n.317+13211A>G		intron_variant	Intron 4 of 5
LINC02572	ENST00000810007.1	n.112+8684A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62171 AN: 151784 Hom.: 13406 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.410 AC: 62265 AN: 151902 Hom.: 13449 Cov.: 32 AF XY: 0.404 AC XY: 29991 AN XY: 74222

African (AFR) AF: 0.548 AC: 22696 AN: 41416

American (AMR) AF: 0.389 AC: 5935 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 952 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1446 AN: 5146

South Asian (SAS) AF: 0.272 AC: 1306 AN: 4808

European-Finnish (FIN) AF: 0.332 AC: 3504 AN: 10552

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25271 AN: 67932

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.384 Hom.: 40125

Bravo AF: 0.420

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7578253; hg19: chr2-130534281;