chr3-190510559-C-T

Variant names:

• chr3-190510559-C-T
• rs9817203

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 0.149 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.148 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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.130

Alfa AF: 0.125 Hom.: 508

Bravo AF: 0.158

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9817203; hg19: chr3-190228348;