chr16-85923808-T-C

Variant names:

• chr16-85923808-T-C
• rs1021479

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0953 AC: 3964 AN: 41574

American (AMR) AF: 0.233 AC: 3567 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1717 AN: 5170

South Asian (SAS) AF: 0.159 AC: 766 AN: 4820

European-Finnish (FIN) AF: 0.0145 AC: 154 AN: 10626

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1165 AN: 68036

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0436 Hom.: 816

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1021479; hg19: chr16-85957414;