rs8051159

Positions:

• chr16-84200625-T-C
• chr16-84200625-T-G

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 0.382 in 152,050 control chromosomes in the GnomAD database, including 11,096 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 0.38 (11096 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 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: 0.381 AC: 57955 AN: 151932 Hom.: 11078 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.382 AC: 58009 AN: 152050 Hom.: 11096 Cov.: 33 AF XY: 0.384 AC XY: 28572 AN XY: 74336

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.366

Alfa AF: 0.375 Hom.: 14783

Bravo AF: 0.379

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8051159; hg19: chr16-84234231;