1-229023085-C-T

Variant names:

• chr1-229023085-C-T
• rs544528
• ENST00000632635.1:n.481-134G>A

Variant summary

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

The ENST00000632635.1(LINC02815):​n.481-134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,190 control chromosomes in the GnomAD database, including 36,837 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 0.70 (36832 hom., cov: 33)
  • Exomes 𝑓: 0.70 (5 hom.)
• Consequence: LINC02815 ENST00000632635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

Genes affected

LINC02815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 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
LINC02815	ENST00000632635.1	n.481-134G>A		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105739 AN: 152052 Hom.: 36799 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.669

GnomAD4 exome AF: 0.700 AC: 14 AN: 20 Hom.: 5 AF XY: 0.688 AC XY: 11 AN XY: 16

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.695 AC: 105811 AN: 152170 Hom.: 36832 Cov.: 33 AF XY: 0.701 AC XY: 52121 AN XY: 74392

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.672

Alfa AF: 0.666 Hom.: 4720

Bravo AF: 0.685

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs544528; hg19: chr1-229158832;