chr3-94243015-A-G

Position:

• chr3-94243015-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 0.157 in 152,132 control chromosomes in the GnomAD database, including 2,047 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 0.16 (2047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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 = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23856 AN: 152016 Hom.: 2033 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.157 AC: 23899 AN: 152132 Hom.: 2047 Cov.: 32 AF XY: 0.156 AC XY: 11585 AN XY: 74392

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.172

Alfa AF: 0.142 Hom.: 782

Bravo AF: 0.162

Asia WGS AF: 0.131 AC: 456 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	0.017
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: rs1584930; hg19: chr3-93961859;