rs166024

Variant names:

• chr5-100618681-A-G
• rs166024

Your query was ambiguous. Multiple possible variants found:

• chr5-100618681-A-G
• chr5-100618681-A-T

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 0.693 in 152,032 control chromosomes in the GnomAD database, including 37,734 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 0.69 (37734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 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: 0.693 AC: 105224 AN: 151914 Hom.: 37702 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.693 AC: 105298 AN: 152032 Hom.: 37734 Cov.: 32 AF XY: 0.696 AC XY: 51678 AN XY: 74296

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.755

Alfa AF: 0.705 Hom.: 4560

Bravo AF: 0.693

Asia WGS AF: 0.811 AC: 2819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166024; hg19: chr5-99954385;