rs7560488

chr2-25345952-T-Cchr2-25345952-T-G

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 0.395 in 151,836 control chromosomes in the GnomAD database, including 12,125 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 0.40 (12125 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 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: 0.395 AC: 59978 AN: 151718 Hom.: 12125 Cov.: 30

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.395 AC: 59990 AN: 151836 Hom.: 12125 Cov.: 30 AF XY: 0.393 AC XY: 29137 AN XY: 74190

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.403

Alfa AF: 0.412 Hom.: 15720

Bravo AF: 0.391

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.59
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7560488; hg19: chr2-25568821;