rs7560488

Variant names:

• chr2-25345952-T-C
• rs7560488

Your query was ambiguous. Multiple possible variants found:

• chr2-25345952-T-C
• chr2-25345952-T-G

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 0.395 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.392 AC: 16217 AN: 41380

American (AMR) AF: 0.346 AC: 5285 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1755 AN: 3464

East Asian (EAS) AF: 0.162 AC: 838 AN: 5178

South Asian (SAS) AF: 0.314 AC: 1509 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4446 AN: 10500

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28504 AN: 67928

Other (OTH) AF: 0.403 AC: 852 AN: 2112

Alfa AF: 0.408 Hom.: 42897

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
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs7560488; hg19: chr2-25568821;