5-56699208-T-G

Variant names:

• chr5-56699208-T-G
• rs16886113

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 0.0832 in 152,252 control chromosomes in the GnomAD database, including 582 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 0.083 (582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 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: 0.0829 AC: 12619 AN: 152134 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0832 AC: 12664 AN: 152252 Hom.: 582 Cov.: 32 AF XY: 0.0825 AC XY: 6140 AN XY: 74442

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0730 Hom.: 631

Bravo AF: 0.0871

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16886113; hg19: chr5-55995035;