3-185639743-C-T

Variant names:

• chr3-185639743-C-T
• rs9864104

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 0.27 in 152,122 control chromosomes in the GnomAD database, including 7,110 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 0.27 (7110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.270 AC: 41076 AN: 152004 Hom.: 7102 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.270 AC: 41127 AN: 152122 Hom.: 7110 Cov.: 33 AF XY: 0.271 AC XY: 20129 AN XY: 74372

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.250

Alfa AF: 0.184 Hom.: 4665

Bravo AF: 0.282

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9864104; hg19: chr3-185357531;