rs11645428

Variant names:

• chr16-81225291-G-A
• rs11645428

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;