rs7583314

Variant names:

• chr2-79084647-C-T
• rs7583314

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 0.515 in 151,882 control chromosomes in the GnomAD database, including 20,529 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 0.52 (20529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78192 AN: 151764 Hom.: 20521 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.515 AC: 78221 AN: 151882 Hom.: 20529 Cov.: 32 AF XY: 0.512 AC XY: 37992 AN XY: 74214

African (AFR) AF: 0.430 AC: 17814 AN: 41414

American (AMR) AF: 0.545 AC: 8305 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2558 AN: 5150

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4814

European-Finnish (FIN) AF: 0.623 AC: 6565 AN: 10532

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37949 AN: 67944

Other (OTH) AF: 0.469 AC: 988 AN: 2108

Alfa AF: 0.533 Hom.: 21995

Bravo AF: 0.509

Asia WGS AF: 0.454 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.37
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7583314; hg19: chr2-79311773;