rs7563245

Variant names:

• chr2-20242870-A-C
• rs7563245

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 0.376 in 151,900 control chromosomes in the GnomAD database, including 10,941 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 0.38 (10941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.377 AC: 57161 AN: 151780 Hom.: 10941 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.376 AC: 57185 AN: 151900 Hom.: 10941 Cov.: 33 AF XY: 0.371 AC XY: 27535 AN XY: 74220

African (AFR) AF: 0.421 AC: 17428 AN: 41412

American (AMR) AF: 0.348 AC: 5314 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1019 AN: 5124

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4820

European-Finnish (FIN) AF: 0.308 AC: 3257 AN: 10564

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25698 AN: 67928

Other (OTH) AF: 0.386 AC: 815 AN: 2110

Alfa AF: 0.376 Hom.: 6578

Bravo AF: 0.381

Asia WGS AF: 0.283 AC: 985 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	1.0
DANN	Benign	0.12
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7563245; hg19: chr2-20442631;