5-166962488-A-G

Position:

• chr5-166962488-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;