rs12216125

chr6-25997230-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606723.2(LINC02980):n.258-673C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TRIM38	XM_005248799.6	c.*9232-673C>T		intron_variant
TRIM38	XM_005248800.6	c.*9232-673C>T		intron_variant
TRIM38	XM_024446303.2	c.*9232-673C>T		intron_variant
TRIM38	XM_047418079.1	c.*9232-673C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02980	ENST00000606723.2	n.258-673C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000608931.1	n.81+1857G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.242

Alfa AF: 0.324 Hom.: 18230

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12216125; hg19: chr6-25997458;