5-166698605-A-G

Variant names:

• chr5-166698605-A-G
• rs441417

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 0.82 in 151,992 control chromosomes in the GnomAD database, including 51,445 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 0.82 (51445 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.820 AC: 124524 AN: 151872 Hom.: 51373 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.820 AC: 124660 AN: 151992 Hom.: 51445 Cov.: 30 AF XY: 0.826 AC XY: 61367 AN XY: 74290

African (AFR) AF: 0.882 AC: 36562 AN: 41446

American (AMR) AF: 0.854 AC: 13030 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2485 AN: 3470

East Asian (EAS) AF: 0.924 AC: 4762 AN: 5156

South Asian (SAS) AF: 0.864 AC: 4161 AN: 4816

European-Finnish (FIN) AF: 0.852 AC: 8996 AN: 10562

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52010 AN: 67966

Other (OTH) AF: 0.815 AC: 1723 AN: 2114

Alfa AF: 0.791 Hom.: 6757

Bravo AF: 0.826

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.012
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs441417; hg19: chr5-166125610;