16-57357042-G-T

Variant names:

• chr16-57357042-G-T
• rs72784894

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 0.0206 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.00631 AC: 262 AN: 41532

American (AMR) AF: 0.0234 AC: 358 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5178

South Asian (SAS) AF: 0.135 AC: 651 AN: 4822

European-Finnish (FIN) AF: 0.0182 AC: 192 AN: 10578

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0160 AC: 1089 AN: 68012

Other (OTH) AF: 0.0190 AC: 40 AN: 2110

Alfa AF: 0.0177 Hom.: 115

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs72784894; hg19: chr16-57390954;