rs9878522

chr3-165407371-T-C

Variant summary

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

The NR_174101.1(LINC01322):n.495+24412T>C 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 0.249 in 152,138 control chromosomes in the GnomAD database, including 4,903 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 0.25 (4903 hom., cov: 32)
• Consequence: LINC01322 NR_174101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01322	NR_174101.1	n.495+24412T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01322	ENST00000470138.5	n.313+24464T>C		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000494915.2	n.549+24412T>C		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000498616.6	n.369+24464T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37896 AN: 152020 Hom.: 4898 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152138 Hom.: 4903 Cov.: 32 AF XY: 0.251 AC XY: 18679 AN XY: 74386

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.232

Alfa AF: 0.227 Hom.: 6612

Bravo AF: 0.248

Asia WGS AF: 0.219 AC: 759 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.36
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878522; hg19: chr3-165125159;