rs10930963

Variant names:

• chr2-181271197-A-G
• rs10930963
• ENST00000424170.5:n.412-16778A>G

Variant summary

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

The ENST00000424170.5(LINC01934):​n.412-16778A>G variant causes a intron 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 ENST00000424170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.358+8220A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.412-16778A>G		intron_variant	Intron 3 of 5	4
LINC01934	ENST00000424655.1	n.104+44662A>G		intron_variant	Intron 2 of 3	3
LINC01934	ENST00000428474.5	n.150+44662A>G		intron_variant	Intron 2 of 3	3

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

African (AFR) AF: 0.604 AC: 25020 AN: 41434

American (AMR) AF: 0.635 AC: 9706 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3468

East Asian (EAS) AF: 0.591 AC: 3060 AN: 5176

South Asian (SAS) AF: 0.661 AC: 3178 AN: 4806

European-Finnish (FIN) AF: 0.623 AC: 6567 AN: 10548

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38054 AN: 67980

Other (OTH) AF: 0.578 AC: 1221 AN: 2114

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10930963; hg19: chr2-182135924;