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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0543 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

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0447

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0729 Hom.: 566

Bravo AF: 0.0531

Asia WGS AF: 0.0160 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17404956; hg19: chr5-166389493;