chr16-9188654-G-A

Variant names:

• chr16-9188654-G-A
• rs10500368

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 0.0986 in 152,142 control chromosomes in the GnomAD database, including 1,608 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 0.099 (1608 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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: 0.0983 AC: 14950 AN: 152024 Hom.: 1596 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0130

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0986 AC: 15007 AN: 152142 Hom.: 1608 Cov.: 33 AF XY: 0.0982 AC XY: 7306 AN XY: 74382

African (AFR) AF: 0.266 AC: 11028 AN: 41462

American (AMR) AF: 0.0838 AC: 1281 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3466

East Asian (EAS) AF: 0.160 AC: 828 AN: 5178

South Asian (SAS) AF: 0.0527 AC: 254 AN: 4822

European-Finnish (FIN) AF: 0.0130 AC: 138 AN: 10604

Middle Eastern (MID) AF: 0.114 AC: 33 AN: 290

European-Non Finnish (NFE) AF: 0.0174 AC: 1181 AN: 68014

Other (OTH) AF: 0.0857 AC: 181 AN: 2112

Alfa AF: 0.0697 Hom.: 135

Bravo AF: 0.111

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs10500368; hg19: chr16-9282511;