ENST00000497379.3:n.76+20807A>G

Variant names:

• chr3-164882802-T-C
• rs1993522
• ENST00000497379.3:n.76+20807A>G

Variant summary

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

The ENST00000497379.3(LINC01324):​n.76+20807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,906 control chromosomes in the GnomAD database, including 7,743 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 0.28 (7743 hom., cov: 32)
• Consequence: LINC01324 ENST00000497379.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 7 publications found

Genes affected

LINC01324 (HGNC:50530): (long intergenic non-protein coding RNA 1324)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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
LINC01324	ENST00000497379.3	n.76+20807A>G		intron_variant	Intron 1 of 4	5
LINC01324	ENST00000715736.1	n.209+15621A>G		intron_variant	Intron 3 of 7
LINC01324	ENST00000722128.1	n.539+15621A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42482 AN: 151788 Hom.: 7728 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.280 AC: 42502 AN: 151906 Hom.: 7743 Cov.: 32 AF XY: 0.287 AC XY: 21330 AN XY: 74196

African (AFR) AF: 0.0673 AC: 2797 AN: 41548

American (AMR) AF: 0.415 AC: 6332 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3462

East Asian (EAS) AF: 0.677 AC: 3463 AN: 5112

South Asian (SAS) AF: 0.359 AC: 1727 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3880 AN: 10534

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22024 AN: 67862

Other (OTH) AF: 0.298 AC: 630 AN: 2114

Alfa AF: 0.304 Hom.: 16283

Bravo AF: 0.277

Asia WGS AF: 0.488 AC: 1693 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.59
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1993522; hg19: chr3-164600590;