chr6-25997230-C-T

Variant names:

• chr6-25997230-C-T
• rs12216125
• ENST00000606723.2:n.258-673C>T

Variant summary

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

The ENST00000606723.2(LINC02980):​n.258-673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,058 control chromosomes in the GnomAD database, including 6,023 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 0.25 (6023 hom., cov: 32)
• Consequence: LINC02980 ENST00000606723.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 40 publications found

Genes affected

LINC02980 (HGNC:56046): (long intergenic non-protein coding RNA 2980)

ENSG00000272558 (HGNC:):

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 = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02980	NR_186641.1	n.253-673C>T		intron_variant	Intron 1 of 2
LINC02980	NR_186642.1	n.253-673C>T		intron_variant	Intron 1 of 2
LINC02980	NR_186643.1	n.253-673C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02980	ENST00000606723.2	n.258-673C>T		intron_variant	Intron 1 of 1	2
ENSG00000272558	ENST00000608931.1	n.81+1857G>A		intron_variant	Intron 1 of 1	3
LINC02980	ENST00000653223.2	n.253-673C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38643 AN: 151940 Hom.: 6025 Cov.: 32

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.254 AC: 38646 AN: 152058 Hom.: 6023 Cov.: 32 AF XY: 0.251 AC XY: 18688 AN XY: 74312

African (AFR) AF: 0.0943 AC: 3915 AN: 41510

American (AMR) AF: 0.222 AC: 3397 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.103 AC: 531 AN: 5180

South Asian (SAS) AF: 0.181 AC: 875 AN: 4830

European-Finnish (FIN) AF: 0.370 AC: 3899 AN: 10538

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24145 AN: 67952

Other (OTH) AF: 0.242 AC: 509 AN: 2102

Alfa AF: 0.316 Hom.: 24293

Bravo AF: 0.238

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs12216125; hg19: chr6-25997458;