16-57418253-A-G

Variant names:

• chr16-57418253-A-G
• rs188872

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 0.802 in 149,562 control chromosomes in the GnomAD database, including 48,823 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 0.80 (48823 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.802 AC: 119849 AN: 149448 Hom.: 48773 Cov.: 24

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.802 AC: 119959 AN: 149562 Hom.: 48823 Cov.: 24 AF XY: 0.795 AC XY: 57890 AN XY: 72824

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.807

Alfa AF: 0.767 Hom.: 23903

Bravo AF: 0.804

Asia WGS AF: 0.703 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs188872; hg19: chr16-57452165;