9-108642554-G-T

Variant names:

• chr9-108642554-G-T
• rs10816693

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 0.472 in 151,996 control chromosomes in the GnomAD database, including 17,373 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 0.47 (17373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 3 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 = 0.772 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71699 AN: 151878 Hom.: 17374 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.472 AC: 71712 AN: 151996 Hom.: 17373 Cov.: 32 AF XY: 0.473 AC XY: 35133 AN XY: 74284

African (AFR) AF: 0.409 AC: 16955 AN: 41432

American (AMR) AF: 0.459 AC: 7007 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4079 AN: 5150

South Asian (SAS) AF: 0.488 AC: 2348 AN: 4810

European-Finnish (FIN) AF: 0.475 AC: 5027 AN: 10576

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33120 AN: 67976

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.476 Hom.: 37446

Bravo AF: 0.471

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10816693; hg19: chr9-111404834;