rs166085

Variant names:

• chr5-92731618-G-A
• rs166085

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 0.645 in 151,816 control chromosomes in the GnomAD database, including 31,825 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 0.64 (31825 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.645 AC: 97831 AN: 151698 Hom.: 31813 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.645 AC: 97881 AN: 151816 Hom.: 31825 Cov.: 31 AF XY: 0.640 AC XY: 47523 AN XY: 74206

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.634

Alfa AF: 0.663 Hom.: 5654

Bravo AF: 0.637

Asia WGS AF: 0.484 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166085; hg19: chr5-92067325; COSMIC: COSV54960464;