chr3-193815412-A-G

Position:

• chr3-193815412-A-G

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 0.298 in 151,838 control chromosomes in the GnomAD database, including 7,833 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 0.30 (7833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.298 AC: 45224 AN: 151720 Hom.: 7831 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.298 AC: 45257 AN: 151838 Hom.: 7833 Cov.: 31 AF XY: 0.293 AC XY: 21728 AN XY: 74220

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.272

Alfa AF: 0.255 Hom.: 2648

Bravo AF: 0.305

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1392705; hg19: chr3-193533201;