chr16-56359279-T-C

Position:

• chr16-56359279-T-C

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 0.649 in 150,918 control chromosomes in the GnomAD database, including 33,575 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 0.65 (33575 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.649 AC: 97885 AN: 150820 Hom.: 33534 Cov.: 28

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.649 AC: 97968 AN: 150918 Hom.: 33575 Cov.: 28 AF XY: 0.644 AC XY: 47417 AN XY: 73604

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.620

Alfa AF: 0.448 Hom.: 1111

Bravo AF: 0.669

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs922446; hg19: chr16-56393191;