5-166530081-T-G

Position:

• chr5-166530081-T-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 0.836 in 152,030 control chromosomes in the GnomAD database, including 55,565 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 (55565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 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: 0.837 AC: 127080 AN: 151912 Hom.: 55542 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.836 AC: 127149 AN: 152030 Hom.: 55565 Cov.: 32 AF XY: 0.841 AC XY: 62465 AN XY: 74316

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.861

Alfa AF: 0.945 Hom.: 94602

Bravo AF: 0.817

Asia WGS AF: 0.839 AC: 2916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2122554; hg19: chr5-165957086;