chr3-42228578-G-C

Position:

• chr3-42228578-G-C

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 0.175 in 152,132 control chromosomes in the GnomAD database, including 4,597 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 0.18 (4597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.175 AC: 26606 AN: 152014 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.175 AC: 26663 AN: 152132 Hom.: 4597 Cov.: 32 AF XY: 0.170 AC XY: 12623 AN XY: 74392

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0744

Gnomad4 OTH AF: 0.145

Alfa AF: 0.142 Hom.: 373

Bravo AF: 0.190

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6809785; hg19: chr3-42270070;