1-229023085-C-T

Variant names:

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

Variant summary

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

The ENST00000632635.1(LINC02814):​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: LINC02814 ENST00000632635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 1 publications found

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

ACMG classification

Our verdict: Benign. The variant received -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
LINC02814	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.600 AC: 6 AN: 10

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.649 AC: 26949 AN: 41504

American (AMR) AF: 0.688 AC: 10515 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2536 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3494 AN: 5174

South Asian (SAS) AF: 0.782 AC: 3771 AN: 4824

European-Finnish (FIN) AF: 0.771 AC: 8170 AN: 10592

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48239 AN: 68000

Other (OTH) AF: 0.672 AC: 1417 AN: 2110

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
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs544528; hg19: chr1-229158832;