chr3-190510559-C-T

Position:

• chr3-190510559-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;