rs9324088

Variant names:

• chr14-106514189-G-A
• rs9324088

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.602 in 150,048 control chromosomes in the GnomAD database, including 27,855 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 (27855 hom., cov: 31)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 6 publications found

Genes affected

IGH (HGNC:5477):

LINC00221 (HGNC:20169): (long intergenic non-protein coding RNA 221)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619530.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00221	ENST00000619530.1	TSL:2	n.1038-6423G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.602 AC: 90225 AN: 149934 Hom.: 27831 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.683

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.602 AC: 90284 AN: 150048 Hom.: 27855 Cov.: 31 AF XY: 0.594 AC XY: 43523 AN XY: 73276

African (AFR) AF: 0.470 AC: 18712 AN: 39810

American (AMR) AF: 0.632 AC: 9600 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2352 AN: 3452

East Asian (EAS) AF: 0.477 AC: 2419 AN: 5068

South Asian (SAS) AF: 0.508 AC: 2427 AN: 4780

European-Finnish (FIN) AF: 0.601 AC: 6356 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 193 AN: 284

European-Non Finnish (NFE) AF: 0.680 AC: 46139 AN: 67898

Other (OTH) AF: 0.633 AC: 1326 AN: 2096

Alfa AF: 0.629 Hom.: 5254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.051
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs9324088; hg19: chr14-106970119;