chr16-57357199-C-T

Variant names:

• chr16-57357199-C-T
• rs77239447

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.093 (640 hom., cov: 10)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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: 0.0932 AC: 6218 AN: 66732 Hom.: 640 Cov.: 10

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0426

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.0931 AC: 6217 AN: 66748 Hom.: 640 Cov.: 10 AF XY: 0.0867 AC XY: 2552 AN XY: 29424

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.0903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77239447; hg19: chr16-57391111;