16-81227181-C-T

Position:

• chr16-81227181-C-T

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 0.42 in 151,824 control chromosomes in the GnomAD database, including 14,082 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 0.42 (14082 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.81227181C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63819 AN: 151708 Hom.: 14084 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.420 AC: 63831 AN: 151824 Hom.: 14082 Cov.: 31 AF XY: 0.413 AC XY: 30644 AN XY: 74200

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.461

Alfa AF: 0.326 Hom.: 867

Bravo AF: 0.416

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9708919; hg19: chr16-81260786;