16-59360890-T-G

Variant names:

• chr16-59360890-T-G
• rs17258247

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 0.103 in 152,216 control chromosomes in the GnomAD database, including 1,584 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 0.10 (1584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.103 AC: 15650 AN: 152098 Hom.: 1583 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.103 AC: 15670 AN: 152216 Hom.: 1584 Cov.: 32 AF XY: 0.107 AC XY: 7949 AN XY: 74424

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.0747

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.0956

Alfa AF: 0.0690 Hom.: 149

Bravo AF: 0.110

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17258247; hg19: chr16-59394794;