16-56691261-A-G

Variant names:

• chr16-56691261-A-G
• rs8064100

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 0.326 in 152,036 control chromosomes in the GnomAD database, including 9,300 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 (9300 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49614 AN: 151918 Hom.: 9298 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.326 AC: 49632 AN: 152036 Hom.: 9300 Cov.: 31 AF XY: 0.323 AC XY: 24037 AN XY: 74306

African (AFR) AF: 0.177 AC: 7349 AN: 41476

American (AMR) AF: 0.307 AC: 4694 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3468

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5176

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4820

European-Finnish (FIN) AF: 0.403 AC: 4252 AN: 10554

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28944 AN: 67950

Other (OTH) AF: 0.334 AC: 705 AN: 2108

Alfa AF: 0.390 Hom.: 54191

Bravo AF: 0.310

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8064100; hg19: chr16-56725173;