chr16-59360890-T-G

Variant names:

• chr16-59360890-T-G
• rs17258247

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.214 AC: 8867 AN: 41512

American (AMR) AF: 0.0747 AC: 1144 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2046 AN: 5164

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4822

European-Finnish (FIN) AF: 0.0399 AC: 423 AN: 10604

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1704 AN: 68022

Other (OTH) AF: 0.0956 AC: 202 AN: 2112

Alfa AF: 0.0733 Hom.: 171

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs17258247; hg19: chr16-59394794;