3-165562421-C-T

Position:

• chr3-165562421-C-T

Variant summary

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

The ENST00000651449.1(LINC01322):​n.374+2047C>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 0.665 in 150,570 control chromosomes in the GnomAD database, including 34,087 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 0.67 (34087 hom., cov: 29)
• Consequence: LINC01322 ENST00000651449.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000651449.1	n.374+2047C>T		intron_variant, non_coding_transcript_variant
LINC01322	ENST00000470138.5	n.408-18438C>T		intron_variant, non_coding_transcript_variant		4
LINC01322	ENST00000496693.1	n.312+13272C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100098 AN: 150446 Hom.: 34049 Cov.: 29

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.665 AC: 100181 AN: 150570 Hom.: 34087 Cov.: 29 AF XY: 0.662 AC XY: 48655 AN XY: 73476

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.672

Alfa AF: 0.623 Hom.: 30760

Bravo AF: 0.676

Asia WGS AF: 0.496 AC: 1717 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523288; hg19: chr3-165280209;