rs7559874

Variant names:

• chr2-191495052-C-T
• rs7559874

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 0.686 in 152,012 control chromosomes in the GnomAD database, including 38,635 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 0.69 (38635 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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: 0.686 AC: 104224 AN: 151894 Hom.: 38637 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.686 AC: 104236 AN: 152012 Hom.: 38635 Cov.: 31 AF XY: 0.681 AC XY: 50599 AN XY: 74306

African (AFR) AF: 0.421 AC: 17422 AN: 41396

American (AMR) AF: 0.644 AC: 9847 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2670 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1983 AN: 5160

South Asian (SAS) AF: 0.699 AC: 3368 AN: 4820

European-Finnish (FIN) AF: 0.827 AC: 8740 AN: 10572

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.849 AC: 57739 AN: 68002

Other (OTH) AF: 0.689 AC: 1453 AN: 2108

Alfa AF: 0.727 Hom.: 32206

Bravo AF: 0.655

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.83
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7559874; hg19: chr2-192359778;