rs8045253

Positions:

• chr16-86404161-T-C
• chr16-86404161-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 0.329 in 152,086 control chromosomes in the GnomAD database, including 8,476 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 0.33 (8476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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: 0.329 AC: 50007 AN: 151968 Hom.: 8481 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.329 AC: 50019 AN: 152086 Hom.: 8476 Cov.: 32 AF XY: 0.323 AC XY: 23999 AN XY: 74368

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.379

Alfa AF: 0.365 Hom.: 13293

Bravo AF: 0.328

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8045253; hg19: chr16-86437767;