chr16-89641688-G-A

Position:

• chr16-89641688-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 0.327 in 151,992 control chromosomes in the GnomAD database, including 10,272 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 0.33 (10272 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.89641688G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHMP1A	ENST00000676275.1	n.524-213C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49744 AN: 151874 Hom.: 10271 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.327 AC: 49736 AN: 151992 Hom.: 10272 Cov.: 32 AF XY: 0.322 AC XY: 23919 AN XY: 74254

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.413

Alfa AF: 0.442 Hom.: 15225

Bravo AF: 0.318

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154657; hg19: chr16-89708096;