rs1400363

Variant names:

• chr4-103329565-A-C
• rs1400363
• ENST00000513793.5:n.136+73271A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513793.5(LINC02428):​n.136+73271A>C variant causes a intron 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 ENST00000513793.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02428	ENST00000513793.5	n.136+73271A>C		intron_variant	Intron 1 of 3	5
LINC02428	ENST00000656104.2	n.508-13527A>C		intron_variant	Intron 1 of 3
LINC02428	ENST00000656681.1	n.469+73271A>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.666 AC: 27554 AN: 41382

American (AMR) AF: 0.437 AC: 6662 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5158

South Asian (SAS) AF: 0.438 AC: 2109 AN: 4818

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10542

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28453 AN: 67942

Other (OTH) AF: 0.500 AC: 1051 AN: 2100

Alfa AF: 0.442 Hom.: 7937

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1400363; hg19: chr4-104250722;