16-23834475-C-T

Variant names:

• chr16-23834475-C-T
• rs3760106

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 0.228 in 151,974 control chromosomes in the GnomAD database, including 4,410 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 0.23 (4410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.228 AC: 34620 AN: 151856 Hom.: 4390 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.228 AC: 34674 AN: 151974 Hom.: 4410 Cov.: 32 AF XY: 0.225 AC XY: 16705 AN XY: 74274

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0660

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.248

Alfa AF: 0.207 Hom.: 5626

Bravo AF: 0.249

Asia WGS AF: 0.103 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760106; hg19: chr16-23845796;