chr5-121434224-A-G

Variant names:

• chr5-121434224-A-G
• rs2897433

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 0.626 in 151,784 control chromosomes in the GnomAD database, including 30,488 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 0.63 (30488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94945 AN: 151666 Hom.: 30458 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.626 AC: 95020 AN: 151784 Hom.: 30488 Cov.: 33 AF XY: 0.626 AC XY: 46422 AN XY: 74166

African (AFR) AF: 0.726 AC: 30126 AN: 41498

American (AMR) AF: 0.659 AC: 10031 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2196 AN: 3462

East Asian (EAS) AF: 0.282 AC: 1456 AN: 5164

South Asian (SAS) AF: 0.669 AC: 3222 AN: 4818

European-Finnish (FIN) AF: 0.567 AC: 5980 AN: 10538

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39850 AN: 67762

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.487 Hom.: 1393

Bravo AF: 0.637

Asia WGS AF: 0.494 AC: 1710 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.57
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2897433; hg19: chr5-120769919;