rs1450534

Variant names:

• chr3-161469877-G-A
• rs1450534

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 0.109 in 152,132 control chromosomes in the GnomAD database, including 2,035 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 0.11 (2035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.109 AC: 16510 AN: 152014 Hom.: 2024 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0738

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.00621

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.109 AC: 16554 AN: 152132 Hom.: 2035 Cov.: 32 AF XY: 0.109 AC XY: 8073 AN XY: 74396

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0830

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.00621

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0699 Hom.: 154

Bravo AF: 0.119

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450534; hg19: chr3-161187665;