rs1599823

Variant names:

• chr16-56641905-T-C
• rs1599823

Your query was ambiguous. Multiple possible variants found:

• chr16-56641905-T-C
• chr16-56641905-T-G

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 0.562 in 152,064 control chromosomes in the GnomAD database, including 25,339 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 0.56 (25339 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 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: 0.562 AC: 85440 AN: 151946 Hom.: 25333 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.562 AC: 85464 AN: 152064 Hom.: 25339 Cov.: 33 AF XY: 0.565 AC XY: 42024 AN XY: 74316

African (AFR) AF: 0.364 AC: 15072 AN: 41440

American (AMR) AF: 0.621 AC: 9491 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2520 AN: 5178

South Asian (SAS) AF: 0.519 AC: 2495 AN: 4808

European-Finnish (FIN) AF: 0.714 AC: 7549 AN: 10580

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44269 AN: 67990

Other (OTH) AF: 0.577 AC: 1217 AN: 2108

Alfa AF: 0.614 Hom.: 77054

Bravo AF: 0.550

Asia WGS AF: 0.519 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		0.023

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs1599823; hg19: chr16-56675817;