5-2202071-A-G

Variant names:

• chr5-2202071-A-G
• rs2897241

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 0.646 in 152,162 control chromosomes in the GnomAD database, including 32,015 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 0.65 (32015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98249 AN: 152042 Hom.: 31979 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.646 AC: 98335 AN: 152162 Hom.: 32015 Cov.: 33 AF XY: 0.643 AC XY: 47799 AN XY: 74374

African (AFR) AF: 0.689 AC: 28582 AN: 41504

American (AMR) AF: 0.695 AC: 10640 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2239 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3150 AN: 5164

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4820

European-Finnish (FIN) AF: 0.662 AC: 7004 AN: 10582

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42791 AN: 67998

Other (OTH) AF: 0.649 AC: 1373 AN: 2116

Alfa AF: 0.628 Hom.: 18561

Bravo AF: 0.656

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.35
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2897241; hg19: chr5-2202185;