22-18044023-T-G

Variant names:

• chr22-18044023-T-G
• rs462904
• ENST00000801735.1:n.548T>G

Variant summary

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

The ENST00000801735.1(LINC01634):​n.548T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,054 control chromosomes in the GnomAD database, including 30,394 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 0.63 (30394 hom., cov: 32)
• Consequence: LINC01634 ENST00000801735.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 10 publications found

Genes affected

LINC01634 (HGNC:52421): (long intergenic non-protein coding RNA 1634)

ENSG00000304254 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.759 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
LINC01634	ENST00000801735.1	n.548T>G		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01634	ENST00000801736.1	n.442T>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000304254	ENST00000801416.1	n.-160T>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95588 AN: 151936 Hom.: 30364 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.629 AC: 95674 AN: 152054 Hom.: 30394 Cov.: 32 AF XY: 0.631 AC XY: 46908 AN XY: 74330

African (AFR) AF: 0.704 AC: 29210 AN: 41470

American (AMR) AF: 0.611 AC: 9314 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4032 AN: 5176

South Asian (SAS) AF: 0.636 AC: 3064 AN: 4818

European-Finnish (FIN) AF: 0.614 AC: 6493 AN: 10576

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39859 AN: 67978

Other (OTH) AF: 0.594 AC: 1254 AN: 2110

Alfa AF: 0.595 Hom.: 102345

Bravo AF: 0.631

Asia WGS AF: 0.679 AC: 2359 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	1.5
DANN	Benign	0.59
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs462904; hg19: chr22-18526789;