chr16-56951602-G-A

Variant names:

• chr16-56951602-G-A
• rs72786786

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 0.243 in 152,052 control chromosomes in the GnomAD database, including 5,250 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 0.24 (5250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.243 AC: 36987 AN: 151934 Hom.: 5250 Cov.: 31

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.243 AC: 36992 AN: 152052 Hom.: 5250 Cov.: 31 AF XY: 0.246 AC XY: 18287 AN XY: 74306

African (AFR) AF: 0.0940 AC: 3901 AN: 41498

American (AMR) AF: 0.265 AC: 4055 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3466

East Asian (EAS) AF: 0.191 AC: 983 AN: 5148

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4814

European-Finnish (FIN) AF: 0.306 AC: 3239 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21311 AN: 67950

Other (OTH) AF: 0.233 AC: 492 AN: 2112

Alfa AF: 0.289 Hom.: 12170

Bravo AF: 0.232

Asia WGS AF: 0.241 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs72786786; hg19: chr16-56985514;