rs7592330

Variant names:

• chr2-68419651-G-A
• rs7592330

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 0.571 in 151,978 control chromosomes in the GnomAD database, including 25,435 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 0.57 (25435 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86616 AN: 151860 Hom.: 25394 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.571 AC: 86706 AN: 151978 Hom.: 25435 Cov.: 31 AF XY: 0.578 AC XY: 42950 AN XY: 74274

African (AFR) AF: 0.492 AC: 20378 AN: 41412

American (AMR) AF: 0.687 AC: 10489 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2422 AN: 3464

East Asian (EAS) AF: 0.899 AC: 4653 AN: 5176

South Asian (SAS) AF: 0.745 AC: 3587 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5699 AN: 10538

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37474 AN: 67978

Other (OTH) AF: 0.610 AC: 1291 AN: 2116

Alfa AF: 0.568 Hom.: 71628

Bravo AF: 0.579

Asia WGS AF: 0.811 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.72
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs7592330; hg19: chr2-68646783;