16-35204369-T-C

Position:

• chr16-35204369-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 0.0144 in 152,286 control chromosomes in the GnomAD database, including 23 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 0.014 (23 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0644 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: 0.0144 AC: 2195 AN: 152170 Hom.: 23 Cov.: 33

Gnomad AFR AF: 0.00422

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0144 AC: 2196 AN: 152286 Hom.: 23 Cov.: 33 AF XY: 0.0161 AC XY: 1202 AN XY: 74470

Gnomad4 AFR AF: 0.00421

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0704

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0128 Hom.: 10

Bravo AF: 0.0152

Asia WGS AF: 0.0540 AC: 187 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7186710; hg19: chr16-34438740;