16-10256280-A-G

Variant names:

• chr16-10256280-A-G
• rs4456502

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 0.325 in 152,106 control chromosomes in the GnomAD database, including 8,158 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 0.32 (8158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.325 AC: 49355 AN: 151986 Hom.: 8149 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.325 AC: 49397 AN: 152106 Hom.: 8158 Cov.: 32 AF XY: 0.324 AC XY: 24121 AN XY: 74368

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.357

Alfa AF: 0.347 Hom.: 5729

Bravo AF: 0.319

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456502; hg19: chr16-10350137;