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. The variant received -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
• Publications: 4 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=-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

African (AFR) AF: 0.884 AC: 36657 AN: 41484

American (AMR) AF: 0.507 AC: 7727 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1631 AN: 3464

East Asian (EAS) AF: 0.424 AC: 2169 AN: 5118

South Asian (SAS) AF: 0.460 AC: 2206 AN: 4800

European-Finnish (FIN) AF: 0.405 AC: 4271 AN: 10534

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34417 AN: 67938

Other (OTH) AF: 0.598 AC: 1259 AN: 2106

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7624915; hg19: chr3-165339010;