16-16816964-C-T

Position:

• chr16-16816964-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 0.121 in 152,188 control chromosomes in the GnomAD database, including 1,196 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 0.12 (1196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18493 AN: 152070 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18487 AN: 152188 Hom.: 1196 Cov.: 32 AF XY: 0.120 AC XY: 8922 AN XY: 74392

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.123

Alfa AF: 0.138 Hom.: 474

Bravo AF: 0.116

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8058794; hg19: chr16-16910821;