rs10930963

chr2-181271197-A-G

Variant summary

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

The NR_130784.1(LINC01934):n.358+8220A>G 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 0.588 in 152,012 control chromosomes in the GnomAD database, including 26,481 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 0.59 (26481 hom., cov: 32)
• Consequence: LINC01934 NR_130784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

LINC01934 (HGNC:52757): (long intergenic non-protein coding RNA 1934)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01934	NR_130784.1	n.358+8220A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01934	ENST00000435411.6	n.358+8220A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89349 AN: 151894 Hom.: 26454 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.588 AC: 89423 AN: 152012 Hom.: 26481 Cov.: 32 AF XY: 0.594 AC XY: 44169 AN XY: 74310

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.578

Alfa AF: 0.588 Hom.: 3863

Bravo AF: 0.589

Asia WGS AF: 0.682 AC: 2369 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	8.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10930963; hg19: chr2-182135924;