6-30848493-G-A

Variant names:

• chr6-30848493-G-A
• rs2535331
• ENST00000442852.2:n.-237C>T

Variant summary

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

The ENST00000442852.2(LINC02570):​n.-237C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,084 control chromosomes in the GnomAD database, including 6,864 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 0.28 (6864 hom., cov: 32)
• Consequence: LINC02570 ENST00000442852.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 23 publications found

Genes affected

LINC02570 (HGNC:39766): (long intergenic non-protein coding RNA 2570)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442852.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02570	ENST00000442852.2	TSL:3	n.-237C>T		upstream_gene	N/A
	LINC02570	ENST00000810494.1		n.-217C>T		upstream_gene	N/A
	LINC02570	ENST00000810497.1		n.-240C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42636 AN: 151968 Hom.: 6866 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.280 AC: 42645 AN: 152084 Hom.: 6864 Cov.: 32 AF XY: 0.282 AC XY: 20926 AN XY: 74320

African (AFR) AF: 0.125 AC: 5186 AN: 41514

American (AMR) AF: 0.245 AC: 3738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1326 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4820

European-Finnish (FIN) AF: 0.392 AC: 4133 AN: 10534

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24664 AN: 67988

Other (OTH) AF: 0.279 AC: 586 AN: 2104

Alfa AF: 0.328 Hom.: 22698

Bravo AF: 0.264

Asia WGS AF: 0.212 AC: 743 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	8.3
DANN	Benign	0.64
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs2535331; hg19: chr6-30816270;