rs823025

Positions:

• chr3-194968684-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 0.196 in 152,182 control chromosomes in the GnomAD database, including 3,386 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 (3386 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.194968684A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29827 AN: 152062 Hom.: 3376 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.196 AC: 29877 AN: 152182 Hom.: 3386 Cov.: 33 AF XY: 0.199 AC XY: 14820 AN XY: 74392

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.165

Alfa AF: 0.149 Hom.: 2471

Bravo AF: 0.194

Asia WGS AF: 0.303 AC: 1051 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	0.029
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs823025; hg19: chr3-194689413;