chr16-23601679-A-G

Variant names:

• chr16-23601679-A-G
• rs3096145

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 0.239 in 151,962 control chromosomes in the GnomAD database, including 4,609 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 (4609 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.239 AC: 36312 AN: 151842 Hom.: 4598 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.239 AC: 36373 AN: 151962 Hom.: 4609 Cov.: 31 AF XY: 0.243 AC XY: 18043 AN XY: 74256

African (AFR) AF: 0.306 AC: 12677 AN: 41416

American (AMR) AF: 0.236 AC: 3602 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1600 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4808

European-Finnish (FIN) AF: 0.261 AC: 2764 AN: 10574

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12798 AN: 67956

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.240 Hom.: 780

Bravo AF: 0.241

Asia WGS AF: 0.296 AC: 1029 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	0.53
DANN	Benign	0.25
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3096145; hg19: chr16-23613000;