rs1502430

chr16-77040450-A-G

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 0.168 in 152,118 control chromosomes in the GnomAD database, including 2,403 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 0.17 (2403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 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: 0.168 AC: 25529 AN: 152000 Hom.: 2405 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.168 AC: 25531 AN: 152118 Hom.: 2403 Cov.: 33 AF XY: 0.170 AC XY: 12642 AN XY: 74368

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.174

Alfa AF: 0.180 Hom.: 314

Bravo AF: 0.161

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502430; hg19: chr16-77074347;