6-30838144-C-T

Variant names:

• chr6-30838144-C-T
• rs3095352
• ENST00000702471.1:n.*180G>A

Variant summary

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

The ENST00000702471.1(LINC02570):​n.*180G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,980 control chromosomes in the GnomAD database, including 18,106 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 0.48 (18106 hom., cov: 32)
• Consequence: LINC02570 ENST00000702471.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 24 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702471.1. 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
	LINC02570	ENST00000702471.1		n.*180G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72233 AN: 151862 Hom.: 18087 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.476 AC: 72293 AN: 151980 Hom.: 18106 Cov.: 32 AF XY: 0.470 AC XY: 34885 AN XY: 74292

African (AFR) AF: 0.349 AC: 14468 AN: 41410

American (AMR) AF: 0.397 AC: 6060 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1701 AN: 5180

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5636 AN: 10558

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39055 AN: 67970

Other (OTH) AF: 0.441 AC: 931 AN: 2110

Alfa AF: 0.539 Hom.: 65640

Bravo AF: 0.463

Asia WGS AF: 0.303 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.53
PhyloP100		-0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3095352;

hg19: chr6-30805921;