rs11398689

Positions:

• chr16-85933613-T-TG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (38608 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85933613_85933614insG		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285163	ENST00000645383.1	n.393+1339_393+1340insG		intron_variant
ENSG00000285163	ENST00000646214.1	n.77+8553_77+8554insG		intron_variant

Frequencies

GnomAD3 genomes AF: 0.719 AC: 104792 AN: 145810 Hom.: 38557 Cov.: 0

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.517

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.719 AC: 104890 AN: 145890 Hom.: 38608 Cov.: 0 AF XY: 0.721 AC XY: 50754 AN XY: 70346

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.659

Alfa AF: 0.482 Hom.: 1077

Asia WGS AF: 0.721 AC: 2496 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11398689; hg19: chr16-85967219;