chr16-57357042-G-T

Position:

• chr16-57357042-G-T

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 0.0206 in 152,192 control chromosomes in the GnomAD database, including 96 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 0.021 (96 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0206 AC: 3129 AN: 152074 Hom.: 95 Cov.: 31

Gnomad AFR AF: 0.00633

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0206 AC: 3130 AN: 152192 Hom.: 96 Cov.: 31 AF XY: 0.0239 AC XY: 1779 AN XY: 74400

Gnomad4 AFR AF: 0.00631

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.0160

Gnomad4 OTH AF: 0.0190

Alfa AF: 0.00945 Hom.: 2

Bravo AF: 0.0161

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72784894; hg19: chr16-57390954;