rs171125

Positions:

• chr16-35526596-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 0.085 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;