chr16-57357022-G-A

Position:

• chr16-57357022-G-A

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 0.13 in 152,100 control chromosomes in the GnomAD database, including 1,550 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 0.13 (1550 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57357022G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19795 AN: 151982 Hom.: 1555 Cov.: 31

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.130 AC: 19781 AN: 152100 Hom.: 1550 Cov.: 31 AF XY: 0.130 AC XY: 9641 AN XY: 74344

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0583 Hom.: 80

Bravo AF: 0.129

Asia WGS AF: 0.212 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34885482; hg19: chr16-57390934;