rs10951138

chr7-26442184-G-A

Variant summary

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

The NR_148499.1(LINC02981):n.630+29945G>A 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 0.246 in 152,134 control chromosomes in the GnomAD database, including 5,234 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 (5234 hom., cov: 33)
• Consequence: LINC02981 NR_148499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

LINC02981 (HGNC:56055): (long intergenic non-protein coding RNA 2981)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02981	NR_148499.1	n.630+29945G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02981	ENST00000702901.1	n.140+29945G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37377 AN: 152016 Hom.: 5235 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.246 AC: 37392 AN: 152134 Hom.: 5234 Cov.: 33 AF XY: 0.247 AC XY: 18399 AN XY: 74390

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.229

Alfa AF: 0.196 Hom.: 5231

Bravo AF: 0.251

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.34
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10951138; hg19: chr7-26481804;