5-41555056-A-G

Variant names:

• chr5-41555056-A-G
• rs822135

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.670

Alfa AF: 0.688 Hom.: 17807

Bravo AF: 0.689

Asia WGS AF: 0.858 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs822135; hg19: chr5-41555158;