rs7602460

Variant names:

• chr2-181397142-A-G
• rs7602460
• ENST00000435411.6:n.591-1237A>G

Variant summary

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

The ENST00000435411.6(LINC01934):​n.591-1237A>G variant causes a intron 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 ENST00000435411.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 16 publications found

Genes affected

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

ENSG00000305978 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.591-1237A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000435411.6	n.591-1237A>G		intron_variant	Intron 4 of 4	5
LINC01934	ENST00000659181.1	n.515-1237A>G		intron_variant	Intron 4 of 4
LINC01934	ENST00000669843.1	n.685-1237A>G		intron_variant	Intron 5 of 5
ENSG00000305978	ENST00000814575.1	n.161-13491T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.577 AC: 23901 AN: 41440

American (AMR) AF: 0.462 AC: 7054 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1172 AN: 5160

South Asian (SAS) AF: 0.488 AC: 2345 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 6993 AN: 10536

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41008 AN: 67932

Other (OTH) AF: 0.528 AC: 1111 AN: 2106

Alfa AF: 0.577 Hom.: 89880

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7602460; hg19: chr2-182261869;