rs7624915

chr3-165621222-A-Cchr3-165621222-A-G

Variant summary

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

The ENST00000651449.1(LINC01322):n.757+4710A>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 0.599 in 151,892 control chromosomes in the GnomAD database, including 29,811 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 0.60 (29811 hom., cov: 31)
• Consequence: LINC01322 ENST00000651449.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01322	ENST00000651449.1	n.757+4710A>C		intron_variant, non_coding_transcript_variant
LINC01322	ENST00000496693.1	n.582+4710A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90862 AN: 151772 Hom.: 29755 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.599 AC: 90967 AN: 151892 Hom.: 29811 Cov.: 31 AF XY: 0.589 AC XY: 43723 AN XY: 74224

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.598

Alfa AF: 0.534 Hom.: 2796

Bravo AF: 0.622

Asia WGS AF: 0.467 AC: 1625 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	0.50
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7624915; hg19: chr3-165339010;