chr16-56947328-G-A

Variant names:

• chr16-56947328-G-A
• rs247611

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 0.287 in 151,906 control chromosomes in the GnomAD database, including 6,431 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 0.29 (6431 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.287 AC: 43624 AN: 151788 Hom.: 6424 Cov.: 30

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.287 AC: 43650 AN: 151906 Hom.: 6431 Cov.: 30 AF XY: 0.289 AC XY: 21426 AN XY: 74244

African (AFR) AF: 0.325 AC: 13471 AN: 41400

American (AMR) AF: 0.312 AC: 4768 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3466

East Asian (EAS) AF: 0.182 AC: 939 AN: 5168

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4814

European-Finnish (FIN) AF: 0.299 AC: 3156 AN: 10560

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17782 AN: 67924

Other (OTH) AF: 0.296 AC: 625 AN: 2112

Alfa AF: 0.281 Hom.: 1051

Bravo AF: 0.290

Asia WGS AF: 0.283 AC: 981 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	0.21
DANN	Benign	0.42
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs247611; hg19: chr16-56981240;