rs1450624

Variant names:

• chr5-166529285-G-A
• rs1450624

Your query was ambiguous. Multiple possible variants found:

• chr5-166529285-G-A
• chr5-166529285-G-C
• chr5-166529285-G-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 0.835 in 151,920 control chromosomes in the GnomAD database, including 55,366 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 (55366 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 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: 0.835 AC: 126803 AN: 151802 Hom.: 55346 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.835 AC: 126870 AN: 151920 Hom.: 55366 Cov.: 30 AF XY: 0.839 AC XY: 62293 AN XY: 74256

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.860

Alfa AF: 0.941 Hom.: 87130

Bravo AF: 0.816

Asia WGS AF: 0.825 AC: 2867 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.97
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450624; hg19: chr5-165956290;