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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.577

Alfa AF: 0.632 Hom.: 48499

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1599823; hg19: chr16-56675817;