rs7624915

Variant names:

• chr3-165621222-A-C
• rs7624915
• ENST00000496693.1:n.582+4710A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-165621222-A-C
• chr3-165621222-A-G

Variant summary

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

The ENST00000496693.1(LINC01322):​n.582+4710A>C variant causes a intron 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 ENST00000496693.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000496693.1	n.582+4710A>C		intron_variant	Intron 3 of 5	5
LINC01322	ENST00000651449.1	n.757+4710A>C		intron_variant	Intron 6 of 8

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;