chr2-181143073-T-C

Position:

• chr2-181143073-T-C

Variant summary

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

The ENST00000414750.1(LINC01934):​n.259+19093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,942 control chromosomes in the GnomAD database, including 17,684 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 0.48 (17684 hom., cov: 32)
• Consequence: LINC01934 ENST00000414750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

Genes affected

LINC01934 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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/exons	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.144+19093T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000414750.1	n.259+19093T>C		intron_variant		3
LINC01934	ENST00000424170.5	n.146+19093T>C		intron_variant		4
LINC01934	ENST00000424655.1	n.39+19093T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72175 AN: 151828 Hom.: 17658 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.475 AC: 72242 AN: 151942 Hom.: 17684 Cov.: 32 AF XY: 0.484 AC XY: 35971 AN XY: 74262

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.463

Alfa AF: 0.439 Hom.: 14515

Bravo AF: 0.477

Asia WGS AF: 0.696 AC: 2407 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018326; hg19: chr2-182007800;