rs1450534

Positions:

• chr3-161469877-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;