rs9817203

Variant names:

• chr3-190510559-C-T
• rs9817203

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 0.149 in 151,958 control chromosomes in the GnomAD database, including 2,866 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 0.15 (2866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.148 AC: 22541 AN: 151840 Hom.: 2856 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.149 AC: 22596 AN: 151958 Hom.: 2866 Cov.: 32 AF XY: 0.149 AC XY: 11100 AN XY: 74268

African (AFR) AF: 0.333 AC: 13805 AN: 41396

American (AMR) AF: 0.111 AC: 1689 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1682 AN: 5162

South Asian (SAS) AF: 0.117 AC: 565 AN: 4818

European-Finnish (FIN) AF: 0.0944 AC: 995 AN: 10544

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3418 AN: 67980

Other (OTH) AF: 0.130 AC: 275 AN: 2108

Alfa AF: 0.159 Hom.: 1595

Bravo AF: 0.158

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.37
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9817203; hg19: chr3-190228348;