5-41555056-A-G

Variant names:

• chr5-41555056-A-G
• rs822135

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 0.692 in 152,056 control chromosomes in the GnomAD database, including 36,747 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 0.69 (36747 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.692 AC: 105098 AN: 151938 Hom.: 36704 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.692 AC: 105194 AN: 152056 Hom.: 36747 Cov.: 31 AF XY: 0.695 AC XY: 51682 AN XY: 74330

African (AFR) AF: 0.646 AC: 26800 AN: 41462

American (AMR) AF: 0.729 AC: 11142 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2027 AN: 3466

East Asian (EAS) AF: 0.980 AC: 5069 AN: 5172

South Asian (SAS) AF: 0.769 AC: 3704 AN: 4818

European-Finnish (FIN) AF: 0.731 AC: 7734 AN: 10578

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.686 AC: 46627 AN: 67954

Other (OTH) AF: 0.670 AC: 1416 AN: 2114

Alfa AF: 0.686 Hom.: 19724

Bravo AF: 0.689

Asia WGS AF: 0.858 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs822135; hg19: chr5-41555158;