chr2-34589070-T-C

Position:

• chr2-34589070-T-C

Variant summary

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

The ENST00000422558.1(LINC01320):​n.476-46179T>C 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 0.871 in 152,052 control chromosomes in the GnomAD database, including 58,257 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 0.87 (58257 hom., cov: 32)
• Consequence: LINC01320 ENST00000422558.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000422558.1	n.476-46179T>C		intron_variant, non_coding_transcript_variant		4
LINC01320	ENST00000650021.1	n.220-74704T>C		intron_variant, non_coding_transcript_variant
LINC01320	ENST00000654103.1	n.598-8884T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132379 AN: 151934 Hom.: 58209 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.871 AC: 132485 AN: 152052 Hom.: 58257 Cov.: 32 AF XY: 0.863 AC XY: 64113 AN XY: 74306

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.868

Alfa AF: 0.874 Hom.: 3280

Bravo AF: 0.877

Asia WGS AF: 0.640 AC: 2223 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1220213; hg19: chr2-34814137;