chr16-81227181-C-T

Variant names:

• chr16-81227181-C-T
• rs9708919

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;