rs8058644

Variant names:

• chr16-49862769-C-T
• rs8058644

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.0487 in 152,244 control chromosomes in the GnomAD database, including 271 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 0.049 (271 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.52

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0719 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: 0.0487 AC: 7413 AN: 152126 Hom.: 271 Cov.: 33

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0487 AC: 7413 AN: 152244 Hom.: 271 Cov.: 33 AF XY: 0.0469 AC XY: 3492 AN XY: 74436

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0686 Hom.: 631

Bravo AF: 0.0501

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	21
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8058644; hg19: chr16-49896680;