rs7602460

chr2-181397142-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.591-1237A>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 0.565 in 151,930 control chromosomes in the GnomAD database, including 24,971 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 0.57 (24971 hom., cov: 31)
• Consequence: LINC01934 NR_130784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01934	NR_130784.1	n.591-1237A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01934	ENST00000435411.6	n.591-1237A>G		intron_variant, non_coding_transcript_variant		5
LINC01934	ENST00000659181.1	n.515-1237A>G		intron_variant, non_coding_transcript_variant
LINC01934	ENST00000669843.1	n.685-1237A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85855 AN: 151812 Hom.: 24949 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.565 AC: 85915 AN: 151930 Hom.: 24971 Cov.: 31 AF XY: 0.563 AC XY: 41786 AN XY: 74234

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.528

Alfa AF: 0.577 Hom.: 59953

Bravo AF: 0.548

Asia WGS AF: 0.324 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.3
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7602460; hg19: chr2-182261869;