rs6784190

Positions:

• chr3-165323075-C-T

Variant summary

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

The NR_174101.1(LINC01322):​n.331-59720C>T 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 0.262 in 152,016 control chromosomes in the GnomAD database, including 5,205 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 0.26 (5205 hom., cov: 32)
• Consequence: LINC01322 NR_174101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01322	NR_174101.1	n.331-59720C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01322	ENST00000470138.5	n.201-59720C>T		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000494915.2	n.165-22397C>T		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000498616.6	n.203-22397C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39888 AN: 151898 Hom.: 5209 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.262 AC: 39896 AN: 152016 Hom.: 5205 Cov.: 32 AF XY: 0.266 AC XY: 19738 AN XY: 74292

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.268

Alfa AF: 0.274 Hom.: 1236

Bravo AF: 0.252

Asia WGS AF: 0.278 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.9
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6784190; hg19: chr3-165040863;