rs2354025

Variant names:

• chr16-86633803-C-T
• rs2354025

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 0.284 in 152,124 control chromosomes in the GnomAD database, including 6,900 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 0.28 (6900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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: 0.284 AC: 43211 AN: 152006 Hom.: 6895 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.284 AC: 43239 AN: 152124 Hom.: 6900 Cov.: 32 AF XY: 0.287 AC XY: 21314 AN XY: 74364

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.282

Alfa AF: 0.310 Hom.: 9533

Bravo AF: 0.274

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2354025; hg19: chr16-86667409;