chr1-229155904-T-G

Position:

• chr1-229155904-T-G

Variant summary

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

The ENST00000666388.1(LINC02814):​n.337+41794A>C 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 0.52 in 152,136 control chromosomes in the GnomAD database, including 22,712 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 0.52 (22712 hom., cov: 32)
• Consequence: LINC02814 ENST00000666388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02815	XR_002958488.1	n.415+28146A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02814	ENST00000666388.1	n.337+41794A>C		intron_variant, non_coding_transcript_variant
LINC02814	ENST00000662083.1	n.46+28146A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79099 AN: 152018 Hom.: 22707 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.520 AC: 79120 AN: 152136 Hom.: 22712 Cov.: 32 AF XY: 0.520 AC XY: 38687 AN XY: 74374

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.559

Alfa AF: 0.602 Hom.: 29102

Bravo AF: 0.511

Asia WGS AF: 0.570 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287024; hg19: chr1-229291651;