rs9834548

Variant names:

• chr3-165422159-C-G
• rs9834548
• ENST00000470138.5:n.314-38380C>G

Variant summary

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

The ENST00000470138.5(LINC01322):​n.314-38380C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,706 control chromosomes in the GnomAD database, including 35,393 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 0.68 (35393 hom., cov: 31)
• Consequence: LINC01322 ENST00000470138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 1 publications found

Genes affected

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01322	NR_125764.2	n.491+39252C>G		intron_variant	Intron 3 of 5
LINC01322	NR_174098.1	n.432-38293C>G		intron_variant	Intron 3 of 6
LINC01322	NR_174099.1	n.379+39252C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000470138.5	n.314-38380C>G		intron_variant	Intron 2 of 3	4
LINC01322	ENST00000494915.2	n.550-38380C>G		intron_variant	Intron 4 of 4	4
LINC01322	ENST00000498616.7	n.370-38380C>G		intron_variant	Intron 3 of 6	4

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102959 AN: 151590 Hom.: 35371 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.679 AC: 103028 AN: 151706 Hom.: 35393 Cov.: 31 AF XY: 0.683 AC XY: 50656 AN XY: 74132

African (AFR) AF: 0.720 AC: 29832 AN: 41424

American (AMR) AF: 0.622 AC: 9427 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2393 AN: 3464

East Asian (EAS) AF: 0.875 AC: 4506 AN: 5148

South Asian (SAS) AF: 0.862 AC: 4154 AN: 4820

European-Finnish (FIN) AF: 0.645 AC: 6801 AN: 10550

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43829 AN: 67832

Other (OTH) AF: 0.631 AC: 1327 AN: 2104

Alfa AF: 0.669 Hom.: 4259

Bravo AF: 0.672

Asia WGS AF: 0.840 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.098
DANN	Benign	0.081
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs9834548; hg19: chr3-165139947;