16-85923808-T-C

Position:

• chr16-85923808-T-C

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 0.0766 in 152,310 control chromosomes in the GnomAD database, including 1,070 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 0.077 (1070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11655 AN: 152194 Hom.: 1067 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0766 AC: 11662 AN: 152310 Hom.: 1070 Cov.: 32 AF XY: 0.0829 AC XY: 6171 AN XY: 74476

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0145

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0229 Hom.: 31

Bravo AF: 0.0939

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021479; hg19: chr16-85957414;