rs166024

Positions:

• 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/exons	MANE	UniProt

Ensembl

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