2-67392923-C-G

Variant summary

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

The ENST00000652561.2(LINC01829):n.193+38G>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 0.756 in 152,140 control chromosomes in the GnomAD database, including 44,123 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 0.76 (44123 hom., cov: 32)
• Consequence: LINC01829 ENST00000652561.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

Genes affected

LINC01829 (HGNC:52635): (long intergenic non-protein coding RNA 1829)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01829	ENST00000652561.2	n.193+38G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114847 AN: 152022 Hom.: 44077 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.756 AC: 114953 AN: 152140 Hom.: 44123 Cov.: 32 AF XY: 0.749 AC XY: 55699 AN XY: 74338

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.772

Alfa AF: 0.637 Hom.: 1994

Bravo AF: 0.766

Asia WGS AF: 0.700 AC: 2435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.75
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6740919; hg19: chr2-67620055;