rs10125054

chr9-112035757-G-Achr9-112035757-G-C

Variant summary

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

The ENST00000658557.1(LINC02977):n.965+2422C>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 0.268 in 152,142 control chromosomes in the GnomAD database, including 5,575 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 0.27 (5575 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC02977 ENST00000658557.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

Genes affected

LINC02977 (HGNC:56036): (long intergenic non-protein coding RNA 2977)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02977	ENST00000658557.1	n.965+2422C>T		intron_variant, non_coding_transcript_variant
LINC02977	ENST00000563434.1	n.1286C>T		non_coding_transcript_exon_variant	2/2	2
LINC02977	ENST00000568421.1	n.554C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40789 AN: 152020 Hom.: 5579 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.268 AC: 40806 AN: 152136 Hom.: 5575 Cov.: 32 AF XY: 0.273 AC XY: 20338 AN XY: 74376

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.276

Alfa AF: 0.248 Hom.: 4968

Bravo AF: 0.266

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10125054; hg19: chr9-114798037; COSMIC: COSV73721038;