rs9834548

chr3-165422159-C-G

Variant summary

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

The NR_174101.1(LINC01322):n.496-38293C>G 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 0.679 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 NR_174101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01322	NR_174101.1	n.496-38293C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01322	ENST00000470138.5	n.314-38380C>G		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000494915.2	n.550-38380C>G		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000498616.6	n.370-38380C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.631

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9834548; hg19: chr3-165139947;