3-16575558-C-G

Position:

• chr3-16575558-C-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 0.16 in 152,108 control chromosomes in the GnomAD database, including 2,396 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 (2396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.160 AC: 24277 AN: 151990 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.160 AC: 24310 AN: 152108 Hom.: 2396 Cov.: 32 AF XY: 0.163 AC XY: 12131 AN XY: 74364

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.139

Alfa AF: 0.138 Hom.: 209

Bravo AF: 0.173

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.0
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6803924; hg19: chr3-16617065;