rs823025

Variant names:

• chr3-194968684-A-G
• rs823025

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.299 AC: 12412 AN: 41514

American (AMR) AF: 0.122 AC: 1860 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1734 AN: 5154

South Asian (SAS) AF: 0.277 AC: 1334 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9497 AN: 68014

Other (OTH) AF: 0.165 AC: 350 AN: 2116

Alfa AF: 0.152 Hom.: 3309

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs823025; hg19: chr3-194689413;