rs625487

Variant names:

• chr5-41561271-C-A
• rs625487

Your query was ambiguous. Multiple possible variants found:

• chr5-41561271-C-A
• chr5-41561271-C-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 0.534 in 151,816 control chromosomes in the GnomAD database, including 23,956 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 0.53 (23956 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.646 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: 0.534 AC: 80959 AN: 151698 Hom.: 23930 Cov.: 30

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.534 AC: 81023 AN: 151816 Hom.: 23956 Cov.: 30 AF XY: 0.536 AC XY: 39740 AN XY: 74206

African (AFR) AF: 0.263 AC: 10899 AN: 41410

American (AMR) AF: 0.654 AC: 9975 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2515 AN: 5118

South Asian (SAS) AF: 0.489 AC: 2352 AN: 4810

European-Finnish (FIN) AF: 0.721 AC: 7590 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44198 AN: 67914

Other (OTH) AF: 0.534 AC: 1128 AN: 2114

Alfa AF: 0.608 Hom.: 41083

Bravo AF: 0.519

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs625487; hg19: chr5-41561373;