1-229122474-G-A

Position:

• chr1-229122474-G-A

Variant summary

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

The ENST00000666388.1(LINC02814):​n.338-29186C>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 0.173 in 152,100 control chromosomes in the GnomAD database, including 3,906 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 (3906 hom., cov: 32)
• Consequence: LINC02814 ENST00000666388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02815	XR_002958488.1	n.416-19599C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02814	ENST00000666388.1	n.338-29186C>T		intron_variant, non_coding_transcript_variant
LINC02814	ENST00000662083.1	n.47-29186C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26327 AN: 151982 Hom.: 3896 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.173 AC: 26368 AN: 152100 Hom.: 3906 Cov.: 32 AF XY: 0.168 AC XY: 12480 AN XY: 74368

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0704 Hom.: 128

Bravo AF: 0.189

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11809337; hg19: chr1-229258221;