rs8057320

Positions:

• chr16-31258230-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 0.63 in 147,426 control chromosomes in the GnomAD database, including 29,891 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 0.63 (29891 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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: 0.631 AC: 92929 AN: 147362 Hom.: 29893 Cov.: 25

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.630 AC: 92944 AN: 147426 Hom.: 29891 Cov.: 25 AF XY: 0.626 AC XY: 44907 AN XY: 71712

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.684

Alfa AF: 0.688 Hom.: 34771

Bravo AF: 0.629

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8057320; hg19: chr16-31269551;