5-166150614-A-G

Position:

• chr5-166150614-A-G

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 0.84 in 152,104 control chromosomes in the GnomAD database, including 56,675 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 0.84 (56675 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.166150614A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254171	ENST00000520075.1	n.252-4544A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127761 AN: 151986 Hom.: 56673 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.840 AC: 127791 AN: 152104 Hom.: 56675 Cov.: 31 AF XY: 0.842 AC XY: 62633 AN XY: 74366

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.871

Alfa AF: 0.933 Hom.: 22987

Bravo AF: 0.812

Asia WGS AF: 0.893 AC: 3107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844221; hg19: chr5-165577619;