rs1371624

Positions:

• chr2-181333260-A-G
• chr2-181333260-A-T

Variant summary

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

The ENST00000424655.1(LINC01934):​n.105-7786A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,902 control chromosomes in the GnomAD database, including 10,150 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 0.36 (10150 hom., cov: 32)
• Consequence: LINC01934 ENST00000424655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LINC01934 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.359-29427A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.582-6412A>G		intron_variant		4
LINC01934	ENST00000424655.1	n.105-7786A>G		intron_variant		3
LINC01934	ENST00000428474.5	n.151-20948A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54816 AN: 151784 Hom.: 10148 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.361 AC: 54833 AN: 151902 Hom.: 10150 Cov.: 32 AF XY: 0.357 AC XY: 26474 AN XY: 74240

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.358

Alfa AF: 0.371 Hom.: 1333

Bravo AF: 0.354

Asia WGS AF: 0.339 AC: 1176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1371624; hg19: chr2-182197987;