16-77539058-C-A

Variant names:

• chr16-77539058-C-A
• rs1826598

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.134 in 152,092 control chromosomes in the GnomAD database, including 1,525 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 0.13 (1525 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.134 AC: 20293 AN: 151974 Hom.: 1523 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.134 AC: 20324 AN: 152092 Hom.: 1525 Cov.: 31 AF XY: 0.133 AC XY: 9860 AN XY: 74372

African (AFR) AF: 0.172 AC: 7114 AN: 41454

American (AMR) AF: 0.229 AC: 3489 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3468

East Asian (EAS) AF: 0.105 AC: 541 AN: 5160

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4824

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7327 AN: 67996

Other (OTH) AF: 0.153 AC: 322 AN: 2108

Alfa AF: 0.120 Hom.: 2000

Bravo AF: 0.151

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.50
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1826598; hg19: chr16-77572955;