rs342817

Variant names:

• chr1-229231439-G-A
• rs342817
• ENST00000651412.1:n.253-3674C>T

Variant summary

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

The ENST00000651412.1(ENSG00000233920):​n.253-3674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,024 control chromosomes in the GnomAD database, including 19,856 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 0.49 (19856 hom., cov: 33)
• Consequence: ENSG00000233920 ENST00000651412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 4 publications found

Genes affected

ENSG00000233920 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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
ENSG00000233920	ENST00000651412.1	n.253-3674C>T		intron_variant	Intron 2 of 3
LINC02814	ENST00000716801.1	n.91+27593C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73862 AN: 151902 Hom.: 19804 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.487 AC: 73976 AN: 152024 Hom.: 19856 Cov.: 33 AF XY: 0.487 AC XY: 36207 AN XY: 74304

African (AFR) AF: 0.729 AC: 30238 AN: 41452

American (AMR) AF: 0.471 AC: 7201 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2785 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4215 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24761 AN: 67976

Other (OTH) AF: 0.443 AC: 937 AN: 2116

Alfa AF: 0.391 Hom.: 7336

Bravo AF: 0.508

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs342817; hg19: chr1-229367186;