2-67392923-C-G

Variant names:

• chr2-67392923-C-G
• rs6740919
• ENST00000652561.2:n.193+38G>C

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01829	ENST00000652561.2	n.193+38G>C		intron_variant	Intron 2 of 9

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;