chr1-229142602-C-A

Position:

• chr1-229142602-C-A

Variant summary

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

The ENST00000666388.1(LINC02814):​n.338-49314G>T 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 0.172 in 152,138 control chromosomes in the GnomAD database, including 3,843 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 0.17 (3843 hom., cov: 32)
• Consequence: LINC02814 ENST00000666388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

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

LINC02815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02815	XR_002958488.1	n.416-39727G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02814	ENST00000666388.1	n.338-49314G>T		intron_variant, non_coding_transcript_variant
LINC02814	ENST00000662083.1	n.46+41448G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26140 AN: 152018 Hom.: 3836 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.172 AC: 26178 AN: 152138 Hom.: 3843 Cov.: 32 AF XY: 0.171 AC XY: 12712 AN XY: 74380

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0410

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0804 Hom.: 1307

Bravo AF: 0.190

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287022; hg19: chr1-229278349;