rs9878522

Variant names:

• chr3-165407371-T-C
• rs9878522
• ENST00000470138.5:n.313+24464T>C

Variant summary

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

The ENST00000470138.5(LINC01322):​n.313+24464T>C variant causes a intron 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 ENST00000470138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 5 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=-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 rank	MANE	Protein	UniProt
LINC01322	NR_125764.2	n.491+24464T>C		intron_variant	Intron 3 of 5
LINC01322	NR_174098.1	n.431+24412T>C		intron_variant	Intron 3 of 6
LINC01322	NR_174099.1	n.379+24464T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000470138.5	n.313+24464T>C		intron_variant	Intron 2 of 3	4
LINC01322	ENST00000494915.2	n.549+24412T>C		intron_variant	Intron 4 of 4	4
LINC01322	ENST00000498616.7	n.369+24464T>C		intron_variant	Intron 3 of 6	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

African (AFR) AF: 0.305 AC: 12662 AN: 41500

American (AMR) AF: 0.241 AC: 3687 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4832

European-Finnish (FIN) AF: 0.207 AC: 2194 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15213 AN: 67976

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.232 Hom.: 10740

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9878522; hg19: chr3-165125159;