3-110322685-G-A

Position:

• chr3-110322685-G-A

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 0.149 in 151,936 control chromosomes in the GnomAD database, including 3,029 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 0.15 (3029 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.149 AC: 22656 AN: 151818 Hom.: 3024 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.149 AC: 22683 AN: 151936 Hom.: 3029 Cov.: 32 AF XY: 0.147 AC XY: 10929 AN XY: 74264

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.144

Alfa AF: 0.103 Hom.: 238

Bravo AF: 0.170

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6788482; hg19: chr3-110041532;