16-35526596-C-T

Variant names:

• chr16-35526596-C-T
• rs171125

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 0.085 in 152,238 control chromosomes in the GnomAD database, including 704 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 0.085 (704 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 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: 0.0851 AC: 12946 AN: 152120 Hom.: 702 Cov.: 33

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.0850 AC: 12946 AN: 152238 Hom.: 704 Cov.: 33 AF XY: 0.0885 AC XY: 6587 AN XY: 74440

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.101 Hom.: 929

Bravo AF: 0.0822

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171125; hg19: chr16-34760967;