rs17404956

Variant names:

• chr5-166962488-A-G
• rs17404956

Your query was ambiguous. Multiple possible variants found:

• chr5-166962488-A-G
• chr5-166962488-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0542 in 152,218 control chromosomes in the GnomAD database, including 280 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 0.054 (280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0831 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: 0.0543 AC: 8255 AN: 152100 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0542 AC: 8249 AN: 152218 Hom.: 280 Cov.: 32 AF XY: 0.0525 AC XY: 3904 AN XY: 74430

African (AFR) AF: 0.0149 AC: 621 AN: 41556

American (AMR) AF: 0.0447 AC: 684 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3466

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5162

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4818

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5775 AN: 67996

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0683 Hom.: 861

Bravo AF: 0.0531

Asia WGS AF: 0.0160 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.66
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs17404956; hg19: chr5-166389493;