rs3760106

chr16-23834475-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 0.228 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;