16-11537909-A-T

Variant names:

• chr16-11537909-A-T
• rs9927783

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 0.382 in 152,012 control chromosomes in the GnomAD database, including 12,558 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 0.38 (12558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.382 AC: 58032 AN: 151894 Hom.: 12522 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.382 AC: 58128 AN: 152012 Hom.: 12558 Cov.: 32 AF XY: 0.382 AC XY: 28372 AN XY: 74306

African (AFR) AF: 0.592 AC: 24559 AN: 41456

American (AMR) AF: 0.317 AC: 4837 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2731 AN: 5156

South Asian (SAS) AF: 0.320 AC: 1540 AN: 4816

European-Finnish (FIN) AF: 0.284 AC: 2998 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19473 AN: 67948

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.343 Hom.: 1233

Bravo AF: 0.396

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.074
DANN	Benign	0.22
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs9927783; hg19: chr16-11631765;