rs16886034

Variant names:

• chr5-56688029-T-C
• rs16886034

Your query was ambiguous. Multiple possible variants found:

• chr5-56688029-T-C
• chr5-56688029-T-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 0.0557 in 152,234 control chromosomes in the GnomAD database, including 280 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 0.056 (280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 (EAS) allele frequency at 95% confidence interval = 0.0969 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: 0.0557 AC: 8476 AN: 152116 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0894

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.0572

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

GnomAD4 genome AF: 0.0557 AC: 8476 AN: 152234 Hom.: 280 Cov.: 32 AF XY: 0.0560 AC XY: 4167 AN XY: 74414

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.0611

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0676

Gnomad4 OTH AF: 0.0594

Alfa AF: 0.0664 Hom.: 356

Bravo AF: 0.0547

Asia WGS AF: 0.105 AC: 365 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	6.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16886034; hg19: chr5-55983856;