rs1400363

chr4-103329565-A-C

Variant summary

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

The ENST00000656681.1(LINC02428):n.469+73271A>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 0.491 in 151,866 control chromosomes in the GnomAD database, including 19,277 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 0.49 (19277 hom., cov: 31)
• Consequence: LINC02428 ENST00000656681.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

LINC02428 (HGNC:53359): (long intergenic non-protein coding RNA 2428)

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 (AFR) allele frequency at 95% confidence interval = 0.659 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
LINC02428	ENST00000656681.1	n.469+73271A>C		intron_variant, non_coding_transcript_variant
LINC02428	ENST00000513793.5	n.136+73271A>C		intron_variant, non_coding_transcript_variant		5
LINC02428	ENST00000656104.1	n.470-13527A>C		intron_variant, non_coding_transcript_variant
LINC02428	ENST00000668077.1	n.243-13527A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74503 AN: 151748 Hom.: 19239 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.491 AC: 74585 AN: 151866 Hom.: 19277 Cov.: 31 AF XY: 0.489 AC XY: 36273 AN XY: 74192

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.500

Alfa AF: 0.443 Hom.: 7173

Bravo AF: 0.500

Asia WGS AF: 0.425 AC: 1480 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	2.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400363; hg19: chr4-104250722;