rs6429432

chr1-235943941-A-C

Variant summary

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

The NR_183724.1(LINC02768):n.873+13941T>G 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 0.929 in 152,480 control chromosomes in the GnomAD database, including 65,926 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 0.93 (65842 hom., cov: 31)
  • Exomes 𝑓: 0.85 (84 hom.)
• Consequence: LINC02768 NR_183724.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

LINC02768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02768	NR_183724.1	n.873+13941T>G		intron_variant, non_coding_transcript_variant
LOC105373215	XR_002958490.2	n.520-5029A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141337 AN: 152126 Hom.: 65781 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.920

GnomAD4 exome AF: 0.847 AC: 200 AN: 236 Hom.: 84 AF XY: 0.819 AC XY: 131 AN XY: 160

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.837

Gnomad4 NFE exome AF: 0.856

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.929 AC: 141458 AN: 152244 Hom.: 65842 Cov.: 31 AF XY: 0.931 AC XY: 69312 AN XY: 74426

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.921

Alfa AF: 0.924 Hom.: 10242

Bravo AF: 0.931

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6429432; hg19: chr1-236107241;