chr3-193394076-C-T

Position:

• chr3-193394076-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 0.199 in 152,000 control chromosomes in the GnomAD database, including 3,108 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 0.20 (3108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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: 0.199 AC: 30195 AN: 151882 Hom.: 3100 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.199 AC: 30230 AN: 152000 Hom.: 3108 Cov.: 32 AF XY: 0.195 AC XY: 14497 AN XY: 74308

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0938

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.186

Alfa AF: 0.190 Hom.: 5797

Bravo AF: 0.207

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs902192; hg19: chr3-193111865;