2-34405965-C-G

Variant names:

• chr2-34405965-C-G
• rs6543833
• ENST00000422558.1:n.475+21396C>G

Variant summary

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

The ENST00000422558.1(LINC01320):​n.475+21396C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,016 control chromosomes in the GnomAD database, including 34,869 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 0.68 (34869 hom., cov: 32)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 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
LINC01320	ENST00000422558.1	n.475+21396C>G		intron_variant	Intron 2 of 2	4
LINC01320	ENST00000650021.1	n.219+21396C>G		intron_variant	Intron 4 of 6
LINC01320	ENST00000654103.1	n.531+6746C>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102601 AN: 151898 Hom.: 34834 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.676 AC: 102692 AN: 152016 Hom.: 34869 Cov.: 32 AF XY: 0.677 AC XY: 50319 AN XY: 74290

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.670

Alfa AF: 0.532 Hom.: 1416

Bravo AF: 0.673

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6543833; hg19: chr2-34631032;