rs7559874

chr2-191495052-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.689

Alfa AF: 0.796 Hom.: 22657

Bravo AF: 0.655

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7559874; hg19: chr2-192359778;