5-16205092-A-G

Position:

• chr5-16205092-A-G

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 0.901 in 152,232 control chromosomes in the GnomAD database, including 61,892 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 0.90 (61892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137097 AN: 152114 Hom.: 61850 Cov.: 33

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.901 AC: 137191 AN: 152232 Hom.: 61892 Cov.: 33 AF XY: 0.900 AC XY: 66960 AN XY: 74420

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.896

Alfa AF: 0.914 Hom.: 83026

Bravo AF: 0.903

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344720; hg19: chr5-16205201;