rs11645428

chr16-81225291-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 0.257 in 152,042 control chromosomes in the GnomAD database, including 5,981 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 0.26 (5981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.257 AC: 39064 AN: 151924 Hom.: 5985 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.257 AC: 39048 AN: 152042 Hom.: 5981 Cov.: 32 AF XY: 0.252 AC XY: 18735 AN XY: 74334

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.00735

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.297

Alfa AF: 0.319 Hom.: 4973

Bravo AF: 0.248

Asia WGS AF: 0.0830 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
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: rs11645428; hg19: chr16-81258896;