2-181112500-A-G

Variant names:

• chr2-181112500-A-G
• rs6433894
• ENST00000414750.1:n.210+443A>G

Variant summary

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

The ENST00000414750.1(LINC01934):​n.210+443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,050 control chromosomes in the GnomAD database, including 16,404 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 0.46 (16404 hom., cov: 32)
• Consequence: LINC01934 ENST00000414750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000414750.1	n.210+443A>G		intron_variant	Intron 3 of 4	3
LINC01934	ENST00000645995.1	n.931+443A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69158 AN: 151932 Hom.: 16372 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.455 AC: 69232 AN: 152050 Hom.: 16404 Cov.: 32 AF XY: 0.465 AC XY: 34583 AN XY: 74342

African (AFR) AF: 0.468 AC: 19397 AN: 41466

American (AMR) AF: 0.528 AC: 8067 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3796 AN: 5182

South Asian (SAS) AF: 0.638 AC: 3075 AN: 4820

European-Finnish (FIN) AF: 0.477 AC: 5035 AN: 10556

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27313 AN: 67960

Other (OTH) AF: 0.443 AC: 936 AN: 2114

Alfa AF: 0.426 Hom.: 9756

Bravo AF: 0.458

Asia WGS AF: 0.700 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.65
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs6433894; hg19: chr2-181977227;